[med-svn] [iqtree] 01/01: Have the full upstream doc at hand if needed.
Andreas Tille
tille at debian.org
Wed Sep 2 11:51:54 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch upstreamm_full_doc
in repository iqtree.
commit e2c36e78200150fc94879cdda56eafcda72d4888
Author: Andreas Tille <tille at debian.org>
Date: Wed Sep 2 13:51:15 2015 +0200
Have the full upstream doc at hand if needed.
---
debian/Documents_source/bioinformatics.bst | 1493 ++
debian/Documents_source/genephylo.bib | 3453 ++++
debian/Documents_source/heiko.bib | 27235 +++++++++++++++++++++++++++
3 files changed, 32181 insertions(+)
diff --git a/debian/Documents_source/bioinformatics.bst b/debian/Documents_source/bioinformatics.bst
new file mode 100644
index 0000000..f59eb9b
--- /dev/null
+++ b/debian/Documents_source/bioinformatics.bst
@@ -0,0 +1,1493 @@
+%%
+%% This is file `bioinformatics.bst',
+%% generated with the docstrip utility.
+%%
+%% The original source files were:
+%%
+%% merlin.mbs (with options: `,ay,nat,vonx,nm-rev,ed-rev,keyxyr,dt-beg,yr-par,yrp-x,note-yr,vol-bf,vnum-x,volp-com,pre-edn,edpar,blk-tit,pp,ed,ord,jabr,and-xcom,etal-it,nfss')
+%% ----------------------------------------
+%% *** Bioinformatics ***
+%%
+%% Copyright 1994-1999 Patrick W Daly
+ % ===============================================================
+ % IMPORTANT NOTICE:
+ % This bibliographic style (bst) file has been generated from one or
+ % more master bibliographic style (mbs) files, listed above.
+ %
+ % This generated file can be redistributed and/or modified under the terms
+ % of the LaTeX Project Public License Distributed from CTAN
+ % archives in directory macros/latex/base/lppl.txt; either
+ % version 1 of the License, or any later version.
+ % ===============================================================
+ % Name and version information of the main mbs file:
+ % \ProvidesFile{merlin.mbs}[1999/05/28 3.89 (PWD)]
+ % For use with BibTeX version 0.99a or later
+ %-------------------------------------------------------------------
+ % This bibliography style file is intended for texts in ENGLISH
+ % This is an author-year citation style bibliography. As such, it is
+ % non-standard LaTeX, and requires a special package file to function properly.
+ % Such a package is natbib.sty by Patrick W. Daly
+ % The form of the \bibitem entries is
+ % \bibitem[Jones et al.(1990)]{key}...
+ % \bibitem[Jones et al.(1990)Jones, Baker, and Smith]{key}...
+ % The essential feature is that the label (the part in brackets) consists
+ % of the author names, as they should appear in the citation, with the year
+ % in parentheses following. There must be no space before the opening
+ % parenthesis!
+ % With natbib v5.3, a full list of authors may also follow the year.
+ % In natbib.sty, it is possible to define the type of enclosures that is
+ % really wanted (brackets or parentheses), but in either case, there must
+ % be parentheses in the label.
+ % The \cite command functions as follows:
+ % \citet{key} ==>> Jones et al. (1990)
+ % \citet*{key} ==>> Jones, Baker, and Smith (1990)
+ % \citep{key} ==>> (Jones et al., 1990)
+ % \citep*{key} ==>> (Jones, Baker, and Smith, 1990)
+ % \citep[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2)
+ % \citep[e.g.][]{key} ==>> (e.g. Jones et al., 1990)
+ % \citep[e.g.][p. 32]{key} ==>> (e.g. Jones et al., p. 32)
+ % \citeauthor{key} ==>> Jones et al.
+ % \citeauthor*{key} ==>> Jones, Baker, and Smith
+ % \citeyear{key} ==>> 1990
+ %---------------------------------------------------------------------
+
+ENTRY
+ { address
+ author
+ booktitle
+ chapter
+ edition
+ editor
+ howpublished
+ institution
+ journal
+ key
+ month
+ note
+ number
+ organization
+ pages
+ publisher
+ school
+ series
+ title
+ type
+ volume
+ year
+ }
+ {}
+ { label extra.label sort.label short.list }
+
+INTEGERS { output.state before.all mid.sentence after.sentence after.block }
+
+FUNCTION {init.state.consts}
+{ #0 'before.all :=
+ #1 'mid.sentence :=
+ #2 'after.sentence :=
+ #3 'after.block :=
+}
+
+STRINGS { s t }
+
+FUNCTION {output.nonnull}
+{ 's :=
+ output.state mid.sentence =
+ { ", " * write$ }
+ { output.state after.block =
+ { add.period$ write$
+ newline$
+ "\newblock " write$
+ }
+ { output.state before.all =
+ 'write$
+ { add.period$ " " * write$ }
+ if$
+ }
+ if$
+ mid.sentence 'output.state :=
+ }
+ if$
+ s
+}
+
+FUNCTION {output}
+{ duplicate$ empty$
+ 'pop$
+ 'output.nonnull
+ if$
+}
+
+FUNCTION {output.check}
+{ 't :=
+ duplicate$ empty$
+ { pop$ "empty " t * " in " * cite$ * warning$ }
+ 'output.nonnull
+ if$
+}
+
+FUNCTION {fin.entry}
+{ add.period$
+ write$
+ newline$
+}
+
+FUNCTION {new.block}
+{ output.state before.all =
+ 'skip$
+ { after.block 'output.state := }
+ if$
+}
+
+FUNCTION {new.sentence}
+{ output.state after.block =
+ 'skip$
+ { output.state before.all =
+ 'skip$
+ { after.sentence 'output.state := }
+ if$
+ }
+ if$
+}
+
+FUNCTION {add.blank}
+{ " " * before.all 'output.state :=
+}
+
+FUNCTION {date.block}
+{
+ add.blank
+}
+
+FUNCTION {not}
+{ { #0 }
+ { #1 }
+ if$
+}
+
+FUNCTION {and}
+{ 'skip$
+ { pop$ #0 }
+ if$
+}
+
+FUNCTION {or}
+{ { pop$ #1 }
+ 'skip$
+ if$
+}
+
+FUNCTION {new.block.checkb}
+{ empty$
+ swap$ empty$
+ and
+ 'skip$
+ 'new.block
+ if$
+}
+
+FUNCTION {field.or.null}
+{ duplicate$ empty$
+ { pop$ "" }
+ 'skip$
+ if$
+}
+
+FUNCTION {emphasize}
+{ duplicate$ empty$
+ { pop$ "" }
+ { "\emph{" swap$ * "}" * }
+ if$
+}
+
+FUNCTION {bolden}
+{ duplicate$ empty$
+ { pop$ "" }
+ { "\textbf{" swap$ * "}" * }
+ if$
+}
+
+
+FUNCTION {capitalize}
+{ "u" change.case$ "t" change.case$ }
+
+FUNCTION {space.word}
+{ " " swap$ * " " * }
+
+ % Here are the language-specific definitions for explicit words.
+ % Each function has a name bbl.xxx where xxx is the English word.
+ % The language selected here is ENGLISH
+FUNCTION {bbl.and}
+{ "and"}
+
+FUNCTION {bbl.etal}
+{ "et~al." }
+
+FUNCTION {bbl.editors}
+{ "eds." }
+
+FUNCTION {bbl.editor}
+{ "ed." }
+
+FUNCTION {bbl.edby}
+{ "edited by" }
+
+FUNCTION {bbl.edition}
+{ "edition" }
+
+FUNCTION {bbl.volume}
+{ "volume" }
+
+FUNCTION {bbl.of}
+{ "of" }
+
+FUNCTION {bbl.number}
+{ "number" }
+
+FUNCTION {bbl.nr}
+{ "no." }
+
+FUNCTION {bbl.in}
+{ "in" }
+
+FUNCTION {bbl.pages}
+{ "pp." }
+
+FUNCTION {bbl.page}
+{ "p." }
+
+FUNCTION {bbl.chapter}
+{ "chapter" }
+
+FUNCTION {bbl.techrep}
+{ "Technical Report" }
+
+FUNCTION {bbl.mthesis}
+{ "Master's thesis" }
+
+FUNCTION {bbl.phdthesis}
+{ "Ph.D. thesis" }
+
+FUNCTION {bbl.first}
+{ "1st" }
+
+FUNCTION {bbl.second}
+{ "2nd" }
+
+FUNCTION {bbl.third}
+{ "3rd" }
+
+FUNCTION {bbl.fourth}
+{ "4th" }
+
+FUNCTION {bbl.fifth}
+{ "5th" }
+
+FUNCTION {bbl.st}
+{ "st" }
+
+FUNCTION {bbl.nd}
+{ "nd" }
+
+FUNCTION {bbl.rd}
+{ "rd" }
+
+FUNCTION {bbl.th}
+{ "th" }
+
+MACRO {jan} {"January"}
+
+MACRO {feb} {"February"}
+
+MACRO {mar} {"March"}
+
+MACRO {apr} {"April"}
+
+MACRO {may} {"May"}
+
+MACRO {jun} {"June"}
+
+MACRO {jul} {"July"}
+
+MACRO {aug} {"August"}
+
+MACRO {sep} {"September"}
+
+MACRO {oct} {"October"}
+
+MACRO {nov} {"November"}
+
+MACRO {dec} {"December"}
+
+FUNCTION {eng.ord}
+{ duplicate$ "1" swap$ *
+ #-2 #1 substring$ "1" =
+ { bbl.th * }
+ { duplicate$ #-1 #1 substring$
+ duplicate$ "1" =
+ { pop$ bbl.st * }
+ { duplicate$ "2" =
+ { pop$ bbl.nd * }
+ { "3" =
+ { bbl.rd * }
+ { bbl.th * }
+ if$
+ }
+ if$
+ }
+ if$
+ }
+ if$
+}
+
+MACRO {acmcs} {"ACM Comput. Surv."}
+
+MACRO {acta} {"Acta Inf."}
+
+MACRO {cacm} {"Commun. ACM"}
+
+MACRO {ibmjrd} {"IBM J. Res. Dev."}
+
+MACRO {ibmsj} {"IBM Syst.~J."}
+
+MACRO {ieeese} {"IEEE Trans. Softw. Eng."}
+
+MACRO {ieeetc} {"IEEE Trans. Comput."}
+
+MACRO {ieeetcad}
+ {"IEEE Trans. Comput.-Aided Design Integrated Circuits"}
+
+MACRO {ipl} {"Inf. Process. Lett."}
+
+MACRO {jacm} {"J.~ACM"}
+
+MACRO {jcss} {"J.~Comput. Syst. Sci."}
+
+MACRO {scp} {"Sci. Comput. Programming"}
+
+MACRO {sicomp} {"SIAM J. Comput."}
+
+MACRO {tocs} {"ACM Trans. Comput. Syst."}
+
+MACRO {tods} {"ACM Trans. Database Syst."}
+
+MACRO {tog} {"ACM Trans. Gr."}
+
+MACRO {toms} {"ACM Trans. Math. Softw."}
+
+MACRO {toois} {"ACM Trans. Office Inf. Syst."}
+
+MACRO {toplas} {"ACM Trans. Prog. Lang. Syst."}
+
+MACRO {tcs} {"Theoretical Comput. Sci."}
+
+
+INTEGERS { nameptr namesleft numnames }
+
+FUNCTION {format.names}
+{ 's :=
+ "" 't :=
+ #1 'nameptr :=
+ s num.names$ 'numnames :=
+ numnames 'namesleft :=
+ { namesleft #0 > }
+ { s nameptr
+ "{vv~}{ll}{, jj}{, f.}" format.name$
+ 't :=
+ nameptr #1 >
+ {
+ namesleft #1 >
+ { ", " * t * }
+ {
+ s nameptr "{ll}" format.name$ duplicate$ "others" =
+ { 't := }
+ { pop$ }
+ if$
+ t "others" =
+ {
+ " " * bbl.etal emphasize *
+ }
+ { bbl.and
+ space.word * t *
+ }
+ if$
+ }
+ if$
+ }
+ 't
+ if$
+ nameptr #1 + 'nameptr :=
+ namesleft #1 - 'namesleft :=
+ }
+ while$
+}
+
+FUNCTION {format.names.ed}
+{ format.names }
+
+FUNCTION {format.key}
+{ empty$
+ { key field.or.null }
+ { "" }
+ if$
+}
+
+FUNCTION {format.authors}
+{ author empty$
+ { "" }
+ { author format.names }
+ if$
+}
+
+FUNCTION {format.editors}
+{ editor empty$
+ { "" }
+ { editor format.names
+ " (" *
+ editor num.names$ #1 >
+ 'bbl.editors
+ 'bbl.editor
+ if$
+ * ")" *
+ }
+ if$
+}
+
+FUNCTION {format.in.editors}
+{ editor empty$
+ { "" }
+ { editor format.names.ed
+ editor num.names$ #1 >
+ { " (" * bbl.editors * ")" * }
+ { " (" * bbl.editor * ")" * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.note}
+{
+ note empty$
+ { "" }
+ { note #1 #1 substring$
+ duplicate$ "{" =
+ 'skip$
+ { output.state mid.sentence =
+ { "l" }
+ { "u" }
+ if$
+ change.case$
+ }
+ if$
+ note #2 global.max$ substring$ *
+ }
+ if$
+}
+
+FUNCTION {format.title}
+{ title empty$
+ { "" }
+ { title "t" change.case$
+ }
+ if$
+}
+
+FUNCTION {format.full.names}
+{'s :=
+ "" 't :=
+ #1 'nameptr :=
+ s num.names$ 'numnames :=
+ numnames 'namesleft :=
+ { namesleft #0 > }
+ { s nameptr
+ "{vv~}{ll}" format.name$
+ 't :=
+ nameptr #1 >
+ {
+ namesleft #1 >
+ { ", " * t * }
+ {
+ s nameptr "{ll}" format.name$ duplicate$ "others" =
+ { 't := }
+ { pop$ }
+ if$
+ t "others" =
+ {
+ " " * bbl.etal emphasize *
+ }
+ {
+ bbl.and
+ space.word * t *
+ }
+ if$
+ }
+ if$
+ }
+ 't
+ if$
+ nameptr #1 + 'nameptr :=
+ namesleft #1 - 'namesleft :=
+ }
+ while$
+}
+
+FUNCTION {author.editor.key.full}
+{ author empty$
+ { editor empty$
+ { key empty$
+ { cite$ #1 #3 substring$ }
+ 'key
+ if$
+ }
+ { editor format.full.names }
+ if$
+ }
+ { author format.full.names }
+ if$
+}
+
+FUNCTION {author.key.full}
+{ author empty$
+ { key empty$
+ { cite$ #1 #3 substring$ }
+ 'key
+ if$
+ }
+ { author format.full.names }
+ if$
+}
+
+FUNCTION {editor.key.full}
+{ editor empty$
+ { key empty$
+ { cite$ #1 #3 substring$ }
+ 'key
+ if$
+ }
+ { editor format.full.names }
+ if$
+}
+
+FUNCTION {make.full.names}
+{ type$ "book" =
+ type$ "inbook" =
+ or
+ 'author.editor.key.full
+ { type$ "proceedings" =
+ 'editor.key.full
+ 'author.key.full
+ if$
+ }
+ if$
+}
+
+FUNCTION {output.bibitem}
+{ newline$
+ "\bibitem[{" write$
+ label write$
+ ")" make.full.names duplicate$ short.list =
+ { pop$ }
+ { * }
+ if$
+ "}]{" * write$
+ cite$ write$
+ "}" write$
+ newline$
+ ""
+ before.all 'output.state :=
+}
+
+FUNCTION {n.dashify}
+{
+ 't :=
+ ""
+ { t empty$ not }
+ { t #1 #1 substring$ "-" =
+ { t #1 #2 substring$ "--" = not
+ { "--" *
+ t #2 global.max$ substring$ 't :=
+ }
+ { { t #1 #1 substring$ "-" = }
+ { "-" *
+ t #2 global.max$ substring$ 't :=
+ }
+ while$
+ }
+ if$
+ }
+ { t #1 #1 substring$ *
+ t #2 global.max$ substring$ 't :=
+ }
+ if$
+ }
+ while$
+}
+
+FUNCTION {word.in}
+{ bbl.in capitalize
+ " " * }
+
+FUNCTION {format.date}
+{ year duplicate$ empty$
+ { "empty year in " cite$ * "; set to ????" * warning$
+ pop$ "????" }
+ 'skip$
+ if$
+ extra.label *
+ before.all 'output.state :=
+ " (" swap$ * ")" *
+}
+
+FUNCTION {format.btitle}
+{ title emphasize
+}
+
+FUNCTION {tie.or.space.connect}
+{ duplicate$ text.length$ #3 <
+ { "~" }
+ { " " }
+ if$
+ swap$ * *
+}
+
+FUNCTION {either.or.check}
+{ empty$
+ 'pop$
+ { "can't use both " swap$ * " fields in " * cite$ * warning$ }
+ if$
+}
+
+FUNCTION {format.bvolume}
+{ volume empty$
+ { "" }
+ { bbl.volume volume tie.or.space.connect
+ series empty$
+ 'skip$
+ { bbl.of space.word * series emphasize * }
+ if$
+ "volume and number" number either.or.check
+ }
+ if$
+}
+
+FUNCTION {format.number.series}
+{ volume empty$
+ { number empty$
+ { series field.or.null }
+ { output.state mid.sentence =
+ { bbl.number }
+ { bbl.number capitalize }
+ if$
+ number tie.or.space.connect
+ series empty$
+ { "there's a number but no series in " cite$ * warning$ }
+ { bbl.in space.word * series * }
+ if$
+ }
+ if$
+ }
+ { "" }
+ if$
+}
+
+FUNCTION {is.num}
+{ chr.to.int$
+ duplicate$ "0" chr.to.int$ < not
+ swap$ "9" chr.to.int$ > not and
+}
+
+FUNCTION {extract.num}
+{ duplicate$ 't :=
+ "" 's :=
+ { t empty$ not }
+ { t #1 #1 substring$
+ t #2 global.max$ substring$ 't :=
+ duplicate$ is.num
+ { s swap$ * 's := }
+ { pop$ "" 't := }
+ if$
+ }
+ while$
+ s empty$
+ 'skip$
+ { pop$ s }
+ if$
+}
+
+FUNCTION {convert.edition}
+{ edition extract.num "l" change.case$ 's :=
+ s "first" = s "1" = or
+ { bbl.first 't := }
+ { s "second" = s "2" = or
+ { bbl.second 't := }
+ { s "third" = s "3" = or
+ { bbl.third 't := }
+ { s "fourth" = s "4" = or
+ { bbl.fourth 't := }
+ { s "fifth" = s "5" = or
+ { bbl.fifth 't := }
+ { s #1 #1 substring$ is.num
+ { s eng.ord 't := }
+ { edition 't := }
+ if$
+ }
+ if$
+ }
+ if$
+ }
+ if$
+ }
+ if$
+ }
+ if$
+ t
+}
+
+FUNCTION {format.edition}
+{ edition empty$
+ { "" }
+ { output.state mid.sentence =
+ { convert.edition "l" change.case$ " " * bbl.edition * }
+ { convert.edition "t" change.case$ " " * bbl.edition * }
+ if$
+ }
+ if$
+}
+
+INTEGERS { multiresult }
+
+FUNCTION {multi.page.check}
+{ 't :=
+ #0 'multiresult :=
+ { multiresult not
+ t empty$ not
+ and
+ }
+ { t #1 #1 substring$
+ duplicate$ "-" =
+ swap$ duplicate$ "," =
+ swap$ "+" =
+ or or
+ { #1 'multiresult := }
+ { t #2 global.max$ substring$ 't := }
+ if$
+ }
+ while$
+ multiresult
+}
+
+FUNCTION {format.pages}
+{ pages empty$
+ { "" }
+ { pages multi.page.check
+ { bbl.pages pages n.dashify tie.or.space.connect }
+ { bbl.page pages tie.or.space.connect }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.journal.pages}
+{ pages empty$
+ 'skip$
+ { duplicate$ empty$
+ { pop$ format.pages }
+ {
+ ", " *
+ pages n.dashify *
+ }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.vol.num.pages}
+{ volume field.or.null
+ bolden
+ format.journal.pages
+}
+
+FUNCTION {format.chapter.pages}
+{ chapter empty$
+ 'format.pages
+ { type empty$
+ { bbl.chapter }
+ { type "l" change.case$ }
+ if$
+ chapter tie.or.space.connect
+ pages empty$
+ 'skip$
+ { ", " * format.pages * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.in.ed.booktitle}
+{ booktitle empty$
+ { "" }
+ { editor empty$
+ { word.in booktitle emphasize * }
+ { word.in format.in.editors * ", " *
+ booktitle emphasize * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.thesis.type}
+{ type empty$
+ 'skip$
+ { pop$
+ type "t" change.case$
+ }
+ if$
+}
+
+FUNCTION {format.tr.number}
+{ type empty$
+ { bbl.techrep }
+ 'type
+ if$
+ number empty$
+ { "t" change.case$ }
+ { number tie.or.space.connect }
+ if$
+}
+
+FUNCTION {format.article.crossref}
+{
+ word.in
+ " \cite{" * crossref * "}" *
+}
+
+FUNCTION {format.book.crossref}
+{ volume empty$
+ { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
+ word.in
+ }
+ { bbl.volume capitalize
+ volume tie.or.space.connect
+ bbl.of space.word *
+ }
+ if$
+ " \cite{" * crossref * "}" *
+}
+
+FUNCTION {format.incoll.inproc.crossref}
+{
+ word.in
+ " \cite{" * crossref * "}" *
+}
+
+FUNCTION {format.org.or.pub}
+{ 't :=
+ ""
+ address empty$ t empty$ and
+ 'skip$
+ {
+ t empty$
+ { address empty$
+ 'skip$
+ { address * }
+ if$
+ }
+ { t *
+ address empty$
+ 'skip$
+ { ", " * address * }
+ if$
+ }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.publisher.address}
+{ publisher empty$
+ { "empty publisher in " cite$ * warning$
+ ""
+ }
+ { publisher }
+ if$
+ format.org.or.pub
+}
+
+FUNCTION {format.organization.address}
+{ organization empty$
+ { "" }
+ { organization }
+ if$
+ format.org.or.pub
+}
+
+FUNCTION {article}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output
+ format.date "year" output.check
+ date.block
+ format.title "title" output.check
+ new.sentence
+ crossref missing$
+ { journal
+ emphasize
+ "journal" output.check
+ format.vol.num.pages output
+ }
+ { format.article.crossref output.nonnull
+ format.pages output
+ }
+ if$
+ format.note output
+ fin.entry
+}
+
+FUNCTION {book}
+{ output.bibitem
+ author empty$
+ { format.editors "author and editor" output.check
+ editor format.key output
+ }
+ { format.authors output.nonnull
+ crossref missing$
+ { "author and editor" editor either.or.check }
+ 'skip$
+ if$
+ }
+ if$
+ format.date "year" output.check
+ date.block
+ format.btitle "title" output.check
+ crossref missing$
+ { format.bvolume output
+ new.sentence
+ format.number.series output
+ format.edition output
+ format.publisher.address output
+ }
+ {
+ new.sentence
+ format.book.crossref output.nonnull
+ }
+ if$
+ format.note output
+ fin.entry
+}
+
+FUNCTION {booklet}
+{ output.bibitem
+ format.authors output
+ author format.key output
+ format.date "year" output.check
+ date.block
+ format.title "title" output.check
+ new.sentence
+ howpublished output
+ address output
+ format.note output
+ fin.entry
+}
+
+FUNCTION {inbook}
+{ output.bibitem
+ author empty$
+ { format.editors "author and editor" output.check
+ editor format.key output
+ }
+ { format.authors output.nonnull
+ crossref missing$
+ { "author and editor" editor either.or.check }
+ 'skip$
+ if$
+ }
+ if$
+ format.date "year" output.check
+ date.block
+ format.btitle "title" output.check
+ crossref missing$
+ {
+ format.bvolume output
+ format.chapter.pages "chapter and pages" output.check
+ new.sentence
+ format.number.series output
+ format.edition output
+ format.publisher.address output
+ }
+ {
+ format.chapter.pages "chapter and pages" output.check
+ new.sentence
+ format.book.crossref output.nonnull
+ }
+ if$
+ format.note output
+ fin.entry
+}
+
+FUNCTION {incollection}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output
+ format.date "year" output.check
+ date.block
+ format.title "title" output.check
+ new.sentence
+ crossref missing$
+ { format.in.ed.booktitle "booktitle" output.check
+ format.bvolume output
+ format.number.series output
+ format.edition output
+ format.chapter.pages output
+ format.publisher.address output
+ }
+ { format.incoll.inproc.crossref output.nonnull
+ format.chapter.pages output
+ }
+ if$
+ format.note output
+ fin.entry
+}
+
+FUNCTION {inproceedings}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output
+ format.date "year" output.check
+ date.block
+ format.title "title" output.check
+ new.sentence
+ crossref missing$
+ { format.in.ed.booktitle "booktitle" output.check
+ format.bvolume output
+ format.number.series output
+ format.pages output
+ publisher empty$
+ { format.organization.address output }
+ { organization output
+ format.publisher.address output
+ }
+ if$
+ }
+ { format.incoll.inproc.crossref output.nonnull
+ format.pages output
+ }
+ if$
+ format.note output
+ fin.entry
+}
+
+FUNCTION {conference} { inproceedings }
+
+FUNCTION {manual}
+{ output.bibitem
+ format.authors output
+ author format.key output
+ format.date "year" output.check
+ date.block
+ format.btitle "title" output.check
+ new.sentence
+ organization output
+ address output
+ format.edition output
+ format.note output
+ fin.entry
+}
+
+FUNCTION {mastersthesis}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output
+ format.date "year" output.check
+ date.block
+ format.btitle "title" output.check
+ new.sentence
+ bbl.mthesis format.thesis.type output.nonnull
+ school "school" output.check
+ address output
+ format.note output
+ fin.entry
+}
+
+FUNCTION {misc}
+{ output.bibitem
+ format.authors output
+ author format.key output
+ format.date "year" output.check
+ date.block
+ format.title output
+ new.sentence
+ howpublished output
+ format.note output
+ fin.entry
+}
+
+FUNCTION {phdthesis}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output
+ format.date "year" output.check
+ date.block
+ format.btitle "title" output.check
+ new.sentence
+ bbl.phdthesis format.thesis.type output.nonnull
+ school "school" output.check
+ address output
+ format.note output
+ fin.entry
+}
+
+FUNCTION {proceedings}
+{ output.bibitem
+ format.editors output
+ editor format.key output
+ format.date "year" output.check
+ date.block
+ format.btitle "title" output.check
+ format.bvolume output
+ format.number.series output
+ publisher empty$
+ { format.organization.address output }
+ { organization output
+ format.publisher.address output
+ }
+ if$
+ format.note output
+ fin.entry
+}
+
+FUNCTION {techreport}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output
+ format.date "year" output.check
+ date.block
+ format.title "title" output.check
+ new.sentence
+ format.tr.number output.nonnull
+ institution "institution" output.check
+ address output
+ format.note output
+ fin.entry
+}
+
+FUNCTION {unpublished}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output
+ format.date "year" output.check
+ date.block
+ format.title "title" output.check
+ format.note "note" output.check
+ fin.entry
+}
+
+FUNCTION {default.type} { misc }
+
+READ
+
+FUNCTION {sortify}
+{ purify$
+ "l" change.case$
+}
+
+INTEGERS { len }
+
+FUNCTION {chop.word}
+{ 's :=
+ 'len :=
+ s #1 len substring$ =
+ { s len #1 + global.max$ substring$ }
+ 's
+ if$
+}
+
+FUNCTION {format.lab.names}
+{ 's :=
+ "" 't :=
+ s #1 "{vv~}{ll}" format.name$
+ s num.names$ duplicate$
+ #2 >
+ { pop$
+ " " * bbl.etal emphasize *
+ }
+ { #2 <
+ 'skip$
+ { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
+ {
+ " " * bbl.etal emphasize *
+ }
+ { bbl.and space.word * s #2 "{vv~}{ll}" format.name$
+ * }
+ if$
+ }
+ if$
+ }
+ if$
+}
+
+FUNCTION {author.key.label}
+{ author empty$
+ { key empty$
+ { cite$ #1 #3 substring$ }
+ 'key
+ if$
+ }
+ { author format.lab.names }
+ if$
+}
+
+FUNCTION {author.editor.key.label}
+{ author empty$
+ { editor empty$
+ { key empty$
+ { cite$ #1 #3 substring$ }
+ 'key
+ if$
+ }
+ { editor format.lab.names }
+ if$
+ }
+ { author format.lab.names }
+ if$
+}
+
+FUNCTION {editor.key.label}
+{ editor empty$
+ { key empty$
+ { cite$ #1 #3 substring$ }
+ 'key
+ if$
+ }
+ { editor format.lab.names }
+ if$
+}
+
+FUNCTION {calc.short.authors}
+{ type$ "book" =
+ type$ "inbook" =
+ or
+ 'author.editor.key.label
+ { type$ "proceedings" =
+ 'editor.key.label
+ 'author.key.label
+ if$
+ }
+ if$
+ 'short.list :=
+}
+
+FUNCTION {calc.label}
+{ calc.short.authors
+ short.list
+ "("
+ *
+ year duplicate$ empty$
+ short.list key field.or.null = or
+ { pop$ "????" }
+ 'skip$
+ if$
+ *
+ 'label :=
+}
+
+FUNCTION {sort.format.names}
+{ 's :=
+ #1 'nameptr :=
+ ""
+ s num.names$ 'numnames :=
+ numnames 'namesleft :=
+ { namesleft #0 > }
+ { s nameptr
+ "{ll{ }}{ f{ }}{ jj{ }}"
+ format.name$ 't :=
+ nameptr #1 >
+ {
+ " " *
+ namesleft #1 = t "others" = and
+ { "zzzzz" * }
+ { t sortify * }
+ if$
+ }
+ { t sortify * }
+ if$
+ nameptr #1 + 'nameptr :=
+ namesleft #1 - 'namesleft :=
+ }
+ while$
+}
+
+FUNCTION {sort.format.title}
+{ 't :=
+ "A " #2
+ "An " #3
+ "The " #4 t chop.word
+ chop.word
+ chop.word
+ sortify
+ #1 global.max$ substring$
+}
+
+FUNCTION {author.sort}
+{ author empty$
+ { key empty$
+ { "to sort, need author or key in " cite$ * warning$
+ ""
+ }
+ { key sortify }
+ if$
+ }
+ { author sort.format.names }
+ if$
+}
+
+FUNCTION {author.editor.sort}
+{ author empty$
+ { editor empty$
+ { key empty$
+ { "to sort, need author, editor, or key in " cite$ * warning$
+ ""
+ }
+ { key sortify }
+ if$
+ }
+ { editor sort.format.names }
+ if$
+ }
+ { author sort.format.names }
+ if$
+}
+
+FUNCTION {editor.sort}
+{ editor empty$
+ { key empty$
+ { "to sort, need editor or key in " cite$ * warning$
+ ""
+ }
+ { key sortify }
+ if$
+ }
+ { editor sort.format.names }
+ if$
+}
+
+FUNCTION {presort}
+{ calc.label
+ label sortify
+ " "
+ *
+ type$ "book" =
+ type$ "inbook" =
+ or
+ 'author.editor.sort
+ { type$ "proceedings" =
+ 'editor.sort
+ 'author.sort
+ if$
+ }
+ if$
+ #1 entry.max$ substring$
+ 'sort.label :=
+ sort.label
+ *
+ " "
+ *
+ title field.or.null
+ sort.format.title
+ *
+ #1 entry.max$ substring$
+ 'sort.key$ :=
+}
+
+ITERATE {presort}
+
+SORT
+
+STRINGS { last.label next.extra }
+
+INTEGERS { last.extra.num number.label }
+
+FUNCTION {initialize.extra.label.stuff}
+{ #0 int.to.chr$ 'last.label :=
+ "" 'next.extra :=
+ #0 'last.extra.num :=
+ #0 'number.label :=
+}
+
+FUNCTION {forward.pass}
+{ last.label label =
+ { last.extra.num #1 + 'last.extra.num :=
+ last.extra.num int.to.chr$ 'extra.label :=
+ }
+ { "a" chr.to.int$ 'last.extra.num :=
+ "" 'extra.label :=
+ label 'last.label :=
+ }
+ if$
+ number.label #1 + 'number.label :=
+}
+
+FUNCTION {reverse.pass}
+{ next.extra "b" =
+ { "a" 'extra.label := }
+ 'skip$
+ if$
+ extra.label 'next.extra :=
+ extra.label
+ duplicate$ empty$
+ 'skip$
+ { "{\natexlab{" swap$ * "}}" * }
+ if$
+ 'extra.label :=
+ label extra.label * 'label :=
+}
+
+EXECUTE {initialize.extra.label.stuff}
+
+ITERATE {forward.pass}
+
+REVERSE {reverse.pass}
+
+FUNCTION {bib.sort.order}
+{ sort.label
+ " "
+ *
+ year field.or.null sortify
+ *
+ " "
+ *
+ title field.or.null
+ sort.format.title
+ *
+ #1 entry.max$ substring$
+ 'sort.key$ :=
+}
+
+ITERATE {bib.sort.order}
+
+SORT
+
+FUNCTION {begin.bib}
+{ preamble$ empty$
+ 'skip$
+ { preamble$ write$ newline$ }
+ if$
+ "\begin{thebibliography}{" number.label int.to.str$ * "}" *
+ write$ newline$
+ "\expandafter\ifx\csname natexlab\endcsname\relax\def\natexlab#1{#1}\fi"
+ write$ newline$
+}
+
+EXECUTE {begin.bib}
+
+EXECUTE {init.state.consts}
+
+ITERATE {call.type$}
+
+FUNCTION {end.bib}
+{ newline$
+ "\end{thebibliography}" write$ newline$
+}
+
+EXECUTE {end.bib}
+%% End of customized bst file
+%%
+%% End of file `bioinformatics.bst'.
diff --git a/debian/Documents_source/genephylo.bib b/debian/Documents_source/genephylo.bib
new file mode 100644
index 0000000..cb81d3a
--- /dev/null
+++ b/debian/Documents_source/genephylo.bib
@@ -0,0 +1,3453 @@
+%% This BibTeX bibliography file was created using BibDesk.
+%% http://bibdesk.sourceforge.net/
+
+
+%% Created for Minh Bui at 2014-10-24 12:44:33 +0200
+
+
+%% Saved with string encoding Unicode (UTF-8)
+
+
+
+ at article{darriba2012,
+ Author = {Diego Darriba and Taboada, Guillermo and Doallo, Ramon and Posada, David},
+ Date-Added = {2014-10-24 10:43:51 +0000},
+ Date-Modified = {2014-10-24 10:44:33 +0000},
+ Doi = {10.1038/nmeth.2109},
+ ISSN = {1548-7091},
+ Journal = {Nat Meth},
+ Number = {8},
+ Pages = {772--772},
+ Title = {jModelTest 2: more models, new heuristics and parallel computing},
+ Volume = {9},
+ Year = {2012},
+ Bdsk-Url-1 = {http://dx.doi.org/10.1038/nmeth.2109}}
+
+ at article{nguyen2014,
+ Author = {Lam Tung Nguyen and Heiko A. Schmidt and Arndt von Haeseler and Bui Quang Minh},
+ Date-Added = {2014-10-24 10:30:55 +0000},
+ Date-Modified = {2014-10-24 10:32:51 +0000},
+ Journal = {Molecular Biology and Evolution},
+ Title = {IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies},
+ Volume = {in press},
+ Year = {2014}}
+
+ at article{tomas2014,
+ Author = {T. Flouri and F. Izquierdo-Carrasco and D. Darriba and A. J. Aberer and L.-T. Nguyen and B. Q. Minh and A. von Haeseler and A. Stamatakis},
+ Journal = {Systematic Biology},
+ Pages = {accepted},
+ Title = {{The Phylogenetic Likelihood Library}},
+ Volume = 63,
+ Year = 2014}
+
+ at article{AgCo1998,
+ Author = {Alan Agresti and Brent A. Coull},
+ Journal = {The American Statistician},
+ Month = {May},
+ Number = 2,
+ Pages = {119-126},
+ Title = {{Approximate is Better than "Exact" for Interval Estimation of {Binomial} Proportions}},
+ Volume = 52,
+ Year = 1998}
+
+ at book{aho1983,
+ Author = {Alfred~V. Aho and John~E. Hopcroft and Jeffrey~D. Ullman},
+ Isbn = {0-2010-0023-7},
+ Publisher = {Addison Wesley},
+ Title = {Data Structures and Algorithms},
+ Year = 1983}
+
+ at article{ANZ1996,
+ Author = {N.~N. Alexandrov and R. Nussinov and R.~M. Zimmer},
+ Journal = {Pac.Symp.Biocomput.},
+ Keywords = {Algorithms; Amino Acid Sequence; Computer Simulation; Databases, Factual; Molecular Sequence Data; *Protein Folding; *Protein Structure, Secondary; Proteins/*chemistry; Sequence Alignment; Sequence Homology, Amino Acid; Software; Support, Non-U.S. Gov't; Support, U.S. Gov't, P.H.S.; Thermodynamics},
+ Language = {english},
+ Pages = {53--572},
+ Title = {Fast protein fold recognition via sequence to structure alignment and contact capacity potentials},
+ Year = 1996}
+
+ at misc{AlSt2000,
+ Author = {Benjamin Allen and Mike Steel},
+ Howpublished = {Research Report 170, Dept. of Math., University of Canterbury},
+ Month = {August},
+ Title = {{Subtree Transfer Operations and Their Induced Metrics on Evolutionary Trees}},
+ Year = 2000}
+
+ at article{AlRh2003,
+ Author = {Elizabeth S. Allman and John A. Rhodes},
+ Journal = {Mathematical Biosciences},
+ Month = {December},
+ Number = 2,
+ Pages = {113-144},
+ Title = {{Phylogenetic Invariants for the General {Markov} Model of Sequence Mutation}},
+ Volume = 186,
+ Year = 2003}
+
+ at article{ABNGYML1999,
+ Author = {Alon, U. and Barkai, N. and Notterman, D.A. and Gish, K. and Ybarra, S. and Mack, D. and Levine, A.J.},
+ Issn = {0027-8424},
+ Journal = {Proc.Natl.Acad.Sci.U.S.A.},
+ Keywords = {Adenocarcinoma/*genetics; Cluster Analysis; Colonic Neoplasms/*genetics; *Gene Expression Regulation, Neoplastic; Human; *Oligonucleotide Probes;},
+ Language = {english},
+ Number = 12,
+ Pages = {6745--6750},
+ Title = {Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays},
+ Volume = 96,
+ Year = 1999}
+
+ at book{alth1998,
+ Address = {Jena},
+ Author = {Ingo Alth{\"o}fer},
+ Isbn = {3-00-003100-6},
+ Publisher = {Ingo Alth{\"o}fer},
+ Title = {13 Jahre 3-Hirn},
+ Year = 1998}
+
+ at article{AMSZZML1997,
+ Author = {S.~F. Altschul and T.~L. Madden and A.~A. Schaffer and J. Zhang and Z.Zhang and W. Miller and D.~J. Lipman},
+ Issn = {0305-1048},
+ Journal = {Nucleic.Acids.Res.},
+ Keywords = {Algorithms; Amino Acid Sequence; Animal; *Databases, Factual; {DNA}/*chemistry; Human; Molecular Sequence Data; Proteins/*chemistry; *Sequence Alignment; *Software; Support, U.S. Gov't, P.H.S.},
+ Language = {english},
+ Number = 17,
+ Pages = {3389--3402},
+ Title = {{Gapped BLAST and PSI-BLAST: a new generation of protein database search programs}},
+ Volume = 25,
+ Year = 1997}
+
+ at article{AnBr1998,
+ Author = {I. Anderson and A. Brass},
+ Issn = {1367-4803},
+ Journal = {Bioinformatics.},
+ Keywords = {*Algorithms; *Base Sequence; *Databases, Factual; *Information Storage and Retrieval; Predictive Value of Tests; ROC Curve; Sensitivity and Specificity; Software; Support, Non-U.S. Gov't},
+ Language = {english},
+ Number = 4,
+ Pages = {349--356},
+ Title = {Searching {DNA} databases for similarities to {DNA} sequences: when is a match significant?},
+ Volume = 14,
+ Year = 1998}
+
+ at article{AVV1991,
+ Author = {P. Argos and M. Vingron and G. Vogt},
+ Issn = {0269-2139},
+ Journal = {Protein.Eng.},
+ Keywords = {*Amino Acid Sequence; Comparative Study; Consensus Sequence; Molecular Sequence Data; Monte Carlo Method; Peptide Fragments; Sequence Alignment/methods; *Sequence Homology, Nucleic Acid},
+ Language = {english},
+ Number = 4,
+ Pages = {375--383},
+ Title = {{Protein sequence comparison: methods and significance}},
+ Volume = 4,
+ Year = 1991}
+
+ at article{AACBGMT1996,
+ Author = {A. Arneodo and Y. d`Aubenton-Carafa and E. Bacry and P.~V. Gaves and J.~F. Muzy and C. Thermes},
+ Journal = {Physica D},
+ Pages = {291--320},
+ Title = {{Wavelet base fractal analysis of {DNA} sequences}},
+ Volume = 96,
+ Year = 1996}
+
+ at article{auch2006,
+ Author = {Auch, Alexander F. and Henz, Stefan R. and Holland, Barbara R. and G{\"o}ker, Markus},
+ Doi = {10.1186/1471-2105-7-350},
+ Journal = {BMC Bioinformatics},
+ Number = 350,
+ Pdf = {auch2006.mgene.pdf},
+ Title = {Genome {BLAST} distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences},
+ Volume = 7,
+ Year = 2006,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2105-7-350}}
+
+ at article{BBW1997,
+ Author = {Ellen Baake and Michael Baake and Holger Wagner},
+ Journal = {Physical Review Letters},
+ Pages = {559-562},
+ Title = {{The Ising quantum chain is equivalent to a model of biological evolution}},
+ Volume = 78,
+ Year = 1997}
+
+ at article{Baak1998,
+ Author = {Ellen Baake},
+ Issn = {0025-5564},
+ Journal = {Mathematical Biosciences},
+ Keywords = {Base Sequence/genetics; *{Markov} Chains; *Models, Biological; *Phylogeny; Support, Non-U.S. Gov't},
+ Language = {english},
+ Number = 1,
+ Pages = {1-21},
+ Title = {What can and what cannot be inferred from pairwise sequence comparisons?},
+ Volume = 154,
+ Year = 1998}
+
+ at article{BBW1998,
+ Author = {Ellen Baake and Michael Baake and Holger Wagner},
+ Journal = {Physical Reviel Letters},
+ Pages = {1191-1192},
+ Title = {{Quantum mechanics versus classical probability in biological evolution}},
+ Volume = {E57},
+ Year = 1998}
+
+ at article{BaHa1999,
+ Author = {Ellen Baake and Arndt von Haeseler},
+ Journal = {Theoretical Population Biology},
+ Pages = {166-175},
+ Title = {{Distance Measures in Terms of Substitution Processes}},
+ Volume = 55,
+ Year = 1999}
+
+ at article{BaGa2000,
+ Author = {Ellen Baake and Wilfried Gabriel},
+ Journal = {Ann. Rev. Comp. Phys.},
+ Pages = {203-264},
+ Title = {{Biological {Evolution} through mutation, selection, and drift: An introductory review}},
+ Volume = {VII},
+ Year = 2000}
+
+ at article{benson2006,
+ Author = {Benson, Dennis A. and Karsch-Mizrachi, Ilene and Lipman, David J. and Ostell, James and Wheeler, David L.},
+ Doi = {10.1093/nar/gkj157},
+ Journal = {Nucl. Acids Res.},
+ Keywords = {GenBank database},
+ Pages = {D16-D20},
+ Pdf = {benson2006.nar.pdf},
+ Pmid = {16381837},
+ Title = {{GenBank}},
+ Volume = 34,
+ Year = 2006,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1093/nar/gkj157}}
+
+ at article{Bail1951,
+ Author = {Norman~T.~J. Bailey},
+ Journal = {Biometrics},
+ Pages = {268-274},
+ Title = {{Testing the Solubility of {Maximum Likelihood} Equations in the Routine Application of Scoring Methods}},
+ Volume = 7,
+ Year = 1951}
+
+ at book{Bail1990,
+ Author = {Norman T.~J. Bailey},
+ Isbn = {0-471-52368-2},
+ Publisher = {John Wiley \& Sons},
+ Series = {Wiley Classics Library},
+ Title = {{The Elements of Stochastic Processes}},
+ Year = 1990}
+
+ at article{baker2005,
+ Author = {Andrew M. Baker and Jane M. Hughes and John C. Dean and Stuart E. Bunn},
+ Doi = {10.1071/MF04050},
+ Journal = {Marine and Freshwater Research},
+ Number = 6,
+ Pages = {629-640},
+ Pdf = {baker2005.mtDNA.csiro.pdf},
+ Title = {Mitochondrial {DNA} reveals phylogenetic structuring and cryptic diversity in Australian freshwater macroinvertebrate assemblages},
+ Volume = 55,
+ Year = 2004,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1071/MF04050}}
+
+ at book{BaBr1998,
+ Address = {Cambridge London},
+ Author = {Pierre F. Baldi and Soren Brunak},
+ Isbn = {0-262-02442-X},
+ Publisher = {MIT Press},
+ Title = {{Bioinformatics: The machine learning approach}},
+ Year = 1998}
+
+ at article{bandelt1986,
+ Author = {Bandelt, Hans-J{\"u}rgen and Dress, Andreas W. M.},
+ Doi = {10.1016/0196-8858(86)90038-2},
+ Journal = {Adv. Appl. Math.},
+ Pages = {309-343},
+ Pdf = {bandelt1986.adv-appl-math.pdf},
+ Title = {Reconstructing the Shape of a Tree from Observed Dissimilarity Data},
+ Volume = 7,
+ Year = 1986,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1016/0196-8858(86)90038-2}}
+
+ at article{bandelt1995,
+ Author = {Bandelt, Hans-J{\"u}rgen and Forster, Peter and Sykes, Bryan C. and Richards, Martin B.},
+ Journal = {Genetics},
+ Keywords = {phylogenetic networks;; Median Networks; Mitochondrial Portraits},
+ Pages = {743-753},
+ Pdf = {bandelt1995.genetics.pdf},
+ Pmid = {8647407},
+ Title = {Mitochondrial Portraits of Human Populations Using Median Networks},
+ Volume = 141,
+ Year = 1995}
+
+ at article{bandelt1992,
+ Author = {Bandelt, Hans-J{\"u}rgen and Dress, Andreas W. M.},
+ Doi = {10.1016/1055-7903(92)90021-8},
+ Journal = {Mol. Phylogenet. Evol.},
+ Keywords = {Split Decomposition; phylogenetic analysis; distance data},
+ Pages = {242-252},
+ Pdf = {bandelt1992.mpe.pdf},
+ Pmid = {1342941},
+ Title = {Split Decomposition: A new and useful approach to phylogenetic analysis of distance data},
+ Volume = 1,
+ Year = 1992,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1016/1055-7903(92)90021-8}}
+
+ at unpublished{BWF1999,
+ Author = {G. Baudoux, J. Wouters, P. Fischer},
+ Note = {PrePrint},
+ Title = {{A Wavelet-based Method for the Analysis of Protein Sequences}},
+ Year = {1999}}
+
+ at article{Belb1993,
+ Author = {Lee Belbin},
+ Journal = {Biol. Conserv.},
+ Number = 3,
+ Pages = {223-230},
+ Title = {{Environmental representativeness: Regional partitioning and reserve selection}},
+ Volume = 66,
+ Year = 1993}
+
+ at article{BCG2000,
+ Author = {V. Berry and O. Gascuel and G. Caraux},
+ Journal = {Computational Statistics and Data Analysis},
+ Pages = {273-283},
+ Title = {{Choosing the Tree Which Actually Best Explains the Data: Another Look at the Bootstrap in Phylogenetic Reconstruction}},
+ Volume = 38,
+ Year = 2000}
+
+ at incollection{bienstock1995,
+ Author = {Daniel Bienstock and Michael~A. Langston},
+ Booktitle = {Handbooks on Operations Research and Management Science},
+ Pages = {481-502},
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+ Pages = {14863--4868},
+ Title = {Cluster analysis and display of genome-wide expression patterns},
+ Volume = 95,
+ Year = 1998}
+
+ at article{ERPSBCSMTB1998,
+ Author = {Ermolaeva, O. and Rastogi, M. and Pruitt, K.D. and Schuler, G.D. and Bittner, M.L. and Chen, Y. and Simon, R. and Meltzer, P. and Trent, J.M. and Boguski, M.S.},
+ Issn = {1061-4036},
+ Journal = {Nat.Genet.},
+ Keywords = {Computer Communication Networks; *Database Management Systems; Databases, Factual; *Gene Expression; Information Storage and Retrieval; Molecular Biology/*methods; Online Systems; User-Computer Interface; MHDA- 1998/09/10 02:02},
+ Language = {english},
+ Number = 1,
+ Pages = {19-23},
+ Title = {Data management and analysis for gene expression arrays},
+ Volume = 20,
+ Year = 1998}
+
+ at article{esser2004,
+ Abstract = {Analyses of 55 individual and 31 concatenated protein data sets encoded in
+Reclinomonas americana and Marchantia polymorpha mitochondrial genomes revealed that current
+methods for constructing phylogenetic trees are insufficiently sensitive (or artifact-insensitive)
+to ascertain the sister of mitochondria among the current sample of eight {alpha}-proteobacterial
+genomes using mitochondrially-encoded proteins. However, Rhodospirillum rubrum came as close to
+mitochondria as any {alpha}-proteobacterium investigated. This prompted a search for methods to
+directly compare eukaryotic genomes to their prokaryotic counterparts to investigate the origin of
+the mitochondrion and its host from the standpoint of nuclear genes. We examined pairwise amino
+acid sequence identity in comparisons of 6,214 nuclear protein-coding genes from Saccharomyces
+cerevisiae to 177,117 proteins encoded in sequenced genomes from 45 eubacteria and 15
+archaebacteria. The results reveal that [~]75% of yeast genes having homologues among the present
+prokaryotic sample share greater amino acid sequence identity to eubacterial than to
+archaebacterial homologues. At high stringency comparisons, only the eubacterial component of the
+yeast genome is detectable. Our findings indicate that at the levels of overall amino acid sequence
+identity and gene content, yeast shares a sister-group relationship with eubacteria, not with
+archaebacteria, in contrast to the current phylogenetic paradigm based on ribosomal RNA. Among
+eubacteria and archaebacteria, proteobacterial and methanogen genomes, respectively, shared more
+similarity with the yeast genome than other prokaryotic genomes surveyed.},
+ Author = {Esser, Christian and Ahmadinejad, Nahal and Wiegand, Christian and Rotte, Carmen and Sebastiani, Federico and Gelius-Dietrich, Gabriel and Henze, Katrin and Kretschmann, Ernst and Richly, Erik and Leister, Dario and Bryant, David and Steel, Michael A. and Lockhart, Peter J. and Penny, David and Martin, William},
+ Doi = {10.1093/molbev/msh160},
+ Eprint = {http://mbe.oxfordjournals.org/cgi/reprint/21/9/1643.pdf},
+ Journal = {Mol Biol Evol},
+ Number = 9,
+ Pages = {1643-1660},
+ Title = {A Genome Phylogeny for Mitochondria Among {alpha}-Proteobacteria and a Predominantly Eubacterial Ancestry of Yeast Nuclear Genes},
+ Url = {http://mbe.oxfordjournals.org/cgi/content/abstract/21/9/1643},
+ Volume = 21,
+ Year = 2004,
+ Bdsk-Url-1 = {http://mbe.oxfordjournals.org/cgi/content/abstract/21/9/1643},
+ Bdsk-Url-2 = {http://dx.doi.org/10.1093/molbev/msh160}}
+
+ at book{Ewen1979,
+ Address = {Berlin etc.},
+ Author = {Warren~J. Ewens},
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+ Publisher = {Springer},
+ Series = {Biomathematics},
+ Title = {{Mathematical Population Genetics}},
+ Volume = 9,
+ Year = 1979}
+
+ at inproceedings{Ewen1982,
+ Author = {Warren~J. Ewens},
+ Booktitle = {Essays in Statistical Science},
+ Editor = {J. Gani and E.J. Hannah},
+ Pages = {9-17},
+ Series = {Journal of Applied Probability},
+ Title = {Aspects of Population Genetics},
+ Volume = {19A},
+ Year = {1982}}
+
+ at book{EwGr2001,
+ Author = {Warren~J. Ewens and Gregory~R. Grant},
+ Isbn = {0-387-95229-2},
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+ Series = {Statistics for Biology and Health},
+ Title = {Statistical Methods in Bioinformatics: An Introduction},
+ Year = 2001}
+
+ at book{FKPT2003,
+ Address = {Berlin, New York, Heidelberg},
+ Author = {Ludwig Fahrmeier and Rita K{\"u}nstler and Iris Pigeot and Gerhard Tutz},
+ Edition = 4,
+ Isbn = {3-540-44000-3},
+ Publisher = {Springer Verlag},
+ Series = {Springer-Lehrbuch},
+ Title = {{Statistik - Der Weg zur Datenanalyse}},
+ Year = 2003}
+
+ at article{Fait1992,
+ Author = {Daniel~P. Faith},
+ Journal = {Biol. Conserv.},
+ Pages = {1-10},
+ Title = {{Conservation Evaluation and Phylogenetic Diversity}},
+ Volume = 61,
+ Year = 1992}
+
+ at manual{faith1994,
+ Author = {Faith, Daniel P. and Walker, Paul A.},
+ Edition = {2.1},
+ Month = {June},
+ Title = {{DIVERSITY:} A Software Package for Sampling Phylogenetic and Environmental Diversity},
+ Year = 1994}
+
+ at article{faith2001,
+ Author = {Faith, Daniel P. and Trueman, John W. H.},
+ Issn = {1063-5157},
+ Journal = {Syst. Biol.},
+ Number = 3,
+ Pages = {331-350},
+ Pdf = {faith2001.systbiol.pdf},
+ Title = {Towards an Inclusive Philosophy for Phylogenetic Inference},
+ Volume = 50,
+ Year = 2001}
+
+ at article{Fait2002,
+ Author = {Daniel~P. Faith},
+ Journal = {Conservation Biology},
+ Number = 1,
+ Pages = 248,
+ Title = {{Quantifying Biodiversity: a Phylogenetic Perspective}},
+ Volume = 16,
+ Year = 2002}
+
+ at article{faith2004,
+ Author = {Faith, D.P. and Reid, C.A.M. and Hunter, J.},
+ Doi = {10.1111/j.1523-1739.2004.00330.x},
+ Journal = {Conserv. Biol.},
+ Number = 1,
+ Pages = {255-261},
+ Title = {Integrating Phylogenetic Diversity, Complementarity, and Endemism for Conservation Assessment},
+ Volume = 18,
+ Year = 2004,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1523-1739.2004.00330.x}}
+
+ at article{FCCFW2003,
+ Author = {D.~P. Faith and G. Carter and G. Cassis and S. Ferrier and L. Wilkie},
+ Journal = {Environmental Science \& Policy},
+ Number = 3,
+ Pages = {311-328},
+ Title = {{Complementarity, biodiversity viability analysis, and policy-based algorithms for conservation}},
+ Volume = 6,
+ Year = 2003}
+
+ at article{faith2003a,
+ Author = {Faith, Daniel P.},
+ Doi = {10.1034/j.1600-0587.2003.03300.x},
+ Journal = {Ecography},
+ Number = 3,
+ Pages = {374-379},
+ Pdf = {faith2003.ecography.pdf},
+ Title = {Environmental diversity ({ED}) as surrogate information for species-level biodiversity},
+ Volume = 26,
+ Year = 2003,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1034/j.1600-0587.2003.03300.x}}
+
+ at article{faith2006a,
+ Author = {Daniel P. Faith and Andrew M. Baker},
+ Journal = {Evolutionary Bioinformatics Online},
+ Pages = {70-77},
+ Title = {Phylogenetic diversity {(PD)} and biodiversity conservation: Some bioinformatics challenges},
+ Volume = 2,
+ Year = 2006}
+
+ at book{FRVW1999,
+ Address = {Providence, RI},
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+ Classmath = {00B15;92-06;92Bxx},
+ Isbn = {0-8218-0826-5},
+ Keywords = {Molecular biology},
+ Publisher = {AMS, American Mathematical Society},
+ Series = {DIMACS. Series in Discrete Mathematics and Theoretical Computer Science},
+ Title = {Mathematical support for molecular biology. Papers related to the special year 1994-1998},
+ Volume = 7,
+ Year = 1999}
+
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+ Author = {Joe Felsenstein},
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+ Volume = 27,
+ Year = {1978}}
+
+ at article{Fels1981,
+ Author = {Joe Felsenstein},
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+ Volume = 17,
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+ Volume = 146,
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+
+ at book{felsenstein2004,
+ Address = {Sunderland, Massachusetts},
+ Author = {Joe Felsenstein},
+ Isbn = {0-878-931775},
+ Keywords = {Inferring Phylogenies; Phylogenetic Methods},
+ Publisher = {Sinauer Associates},
+ Remark = {felsenstein2003 = felsenstein2004; the book was in the shops in 2003, official date 2004},
+ Title = {{Inferring Phylogenies}},
+ Year = 2004}
+
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+ Publisher = {Academic Press},
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+ Year = 1967}
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+ Volume = 24,
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+
+ at article{gascuel2006,
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+ Volume = {July 28th},
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+ Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msl072}}
+
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+ Issn = {0925-4773},
+ Journal = {Mech.Dev.},
+ Keywords = {Animal; Body Patterning/*genetics; Databases, Factual; Ectoderm; Embryo, Nonmammalian; Embryonic Induction/genetics; Endoderm; Epidermis/embryology; Gastrula; *Gene Expression Regulation, Developmental; Genetic Techniques; In Situ Hybridization/methods; Support, Non-U.S. Gov't; Tail/embryology; Xenopus/*embryology/*genetics},
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+ Number = {1/2},
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+ Title = {Evaluation Measures of Multiple Sequence Alignments},
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+
+ at book{gaston2004,
+ Author = {Gaston, Kevin J. and Spicer, John I.},
+ Edition = {2nd},
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+ Publisher = {Blackwell Publishing Professional},
+ Title = {Biodiversity: An Introduction},
+ Year = 2004}
+
+ at book{graur2000,
+ Address = {Sunderland, Massachusetts},
+ Author = {Dan Graur and Wen-Hsiung Li},
+ Edition = {2nd},
+ Isbn = {0-87893-266-6},
+ Publisher = {Sinauer Associates},
+ Title = {Fundamentals of Molecular Evolution},
+ Year = 2000}
+
+ at techreport{GPS2001,
+ Address = {University of Kaiserslautern},
+ Author = {Gert-Martin Greuel and Gerhard Pfister and Hans Sch\"onemann},
+ Institution = {Centre for Computer Algebra},
+ Note = {{\tt http://www.singular.uni-kl.de}},
+ Title = {{\sc Singular} 2.0},
+ Type = {{A Computer Algebra System for Polynomial Computations}},
+ Year = {2001}}
+
+ at book{GS2001,
+ Author = {Geoffrey Grimmet and David Stirzaker},
+ Edition = 3,
+ Isbn = {0-198-57223-0},
+ Publisher = {Oxford University Press},
+ Title = {{Probability and Random Processes}},
+ Year = 2001}
+
+ at book{GS2001,
+ Author = {Geoffrey Grimmet and David Stirzaker},
+ Isbn = {0-198-57221-2},
+ Publisher = {Oxford University Press},
+ Title = {{One Thousand Exercises in Probability}},
+ Year = 2001}
+
+ at article{GuLi1998,
+ Author = {Gu, X. and Li, W.H.},
+ Issn = {0027-8424},
+ Journal = {Proc.Natl.Acad.Sci.U.S.A.},
+ Keywords = {Animal; {DNA}/analysis/*genetics; *Evolution, Molecular; Human; *Models, Molecular; *Models, Theoretical; Nucleotides/*analysis; Support, U.S. Gov't, P.H.S.},
+ Language = {english},
+ Number = 11,
+ Pages = {5899--5905},
+ Title = {Estimation of {Evolutionary} distances under stationary and nonstationary models of nucleotide substitution},
+ Volume = 95,
+ Year = 1998}
+
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+ Author = {Guermeur, Y. and Geourjon, C. and Gallinari, P. and Deleage, G.},
+ Issn = {1367-4803},
+ Journal = {Bioinformatics.},
+ Keywords = {Amino Acid Sequence; Computer Simulation; Databases, Factual; Models, Molecular; Molecular Sequence Data; *Neural Networks (Computer); Pattern Recognition; *Protein Structure, Secondary},
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+ Number = 5,
+ Pages = {413--421},
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+ Year = 1999}
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+ Author = {St{\'e}phane Guindon and Olivier Gascuel},
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+ Number = 4,
+ Pages = {644-651},
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+ Bdsk-Url-1 = {http://dx.doi.org/10.1080/10635150600873876}}
+
+ at article{hasegawa1985,
+ Author = {Hasegawa, Masami and Kishino, Hirohisa and Yano, Taka--Aki},
+ Doi = {10.1007/BF02101694},
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+ Keywords = {evolution of hominoids; phylogenetic position of Australopithecus afarensis; intersecies transfer of mitochondrial DNA},
+ Pages = {160-174},
+ Pdf = {hasegawa1985.jme.pdf},
+ Pmid = {3934395},
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+ Volume = 22,
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+
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+ Year = 1997}
+
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+ Author = {G. von Heijne},
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+ Keywords = {*Amino Acid Sequence; Animal; *Base Sequence; {DNA}/genetics; Mathematics; *Models, Genetic; Operon; Protein Conformation; RNA/genetics; RNA, Messenger/genetics},
+ Language = {english},
+ Number = 6,
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+ Author = {Henz, Stefan R. and Huson, Daniel H. and Auch, Alexander F. and Nieselt-Struwe, Kay and Schuster, Stephan C.},
+ Doi = {10.1093/bioinformatics/bth324},
+ Journal = {Bioinformatics},
+ Number = 10,
+ Pages = {2329--2335},
+ Pdf = {NONE},
+ Title = {Whole-genome prokaryotic phylogeny},
+ Volume = {21},
+ Year = 2005,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/bth324}}
+
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+ Journal = {Journal of Statistical Physics},
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+
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+ Title = {{Mutation-Selection Balance: Ancestry, Load and Maximum Principle}},
+ Year = 2001}
+
+ at article{hertel2006,
+ Author = {Hertel,Jana and Lindemeyer, Manuela and Missal, Kristin and Fried, Claudia and Tanzer, Andrea and Flamm, Christoph and Hofacker, Ivo L. and Stadler, Peter F. and the students of Bioinformatics Computer Labs 2004/2005},
+ Doi = {10.1186/1471-2164-7-25},
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+ Number = 25,
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+ Title = {The expansion of the metazoan micro{RNA} repertoire},
+ Volume = 7,
+ Year = 2006,
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+ Number = 2,
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+ Address = {New York},
+ Author = {Holland, Barbara and Moulton, Vincent},
+ Booktitle = {Proceedings of the 3rd International Workshop on Algorithms in Bioinformatics (WABI 2003)},
+ Doi = {10.1007/b13243},
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+ Pages = {165-176},
+ Pdf = {holland2003a.LNCS-manuscript.pdf},
+ Publisher = {Springer},
+ Series = {Lecture Notes in Computer Science},
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+ Volume = 2812,
+ Year = 2003,
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+
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+ Address = {Oxford, UK},
+ Author = {Huber, Katharina T. and Moulton, Vincent},
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+ Editor = {Gascuel, Olivier},
+ Keywords = {phylogenetic networks; median networks; visual complexity of networks; consensus networks; tree-likeness; networks from distances; neighbor-net},
+ Pages = {178-204},
+ Pdf = {huber2005.MathEvolPhylogenet-book-proof.pdf},
+ Publisher = {Oxford University Press},
+ Title = {Phylogenetic Networks},
+ Year = 2005}
+
+ at article{huber2001,
+ Author = {Huber, Katharina T. and Moulton, Vincent and Lockhart, Peter J. and Dress, Andreas},
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+ Number = 2,
+ Pages = {302-310},
+ Pdf = {huber2001.mpe.pdf},
+ Title = {Pruned Median Networks: A technique for reducing the complexity of median networks},
+ Volume = 19,
+ Year = 2001,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1006/mpev.2001.0935}}
+
+ at article{HLMR2002,
+ Author = {John P. Huelsenbeck and Bret Larget and Richard E. Miller and Fredrik Ronquist},
+ Journal = {Systematic Biology},
+ Number = 5,
+ Pages = {673-688},
+ Title = {{Potential Applications and Pitfalls of {Bayesian} Inference of Phylogeny}},
+ Volume = 51,
+ Year = 2002}
+
+ at article{HuBo2001,
+ Author = {John~P. Huelsenbeck and Jonathan~P. Bollback},
+ Journal = {Systematic Biology},
+ Number = 3,
+ Pages = {351-366},
+ Title = {{Empirical and Hierarchical {Bayesian} Estimation of Ancestral States}},
+ Volume = 50,
+ Year = 2001}
+
+ at book{Hump1975,
+ Author = {James E. Humphreys},
+ Isbn = {0-387-90108-6},
+ Publisher = {Springer-Verlag},
+ Series = {Graduate Texts in Mathematics},
+ Title = {{Linear algebraic groups}},
+ Year = 1975}
+
+ at article{HWV1995,
+ Author = {Christopher~J. Humphries and Paul~H. Williams and Richard~I. Vane-Wright},
+ Journal = {Annu. Rev. Ecol. Syst.},
+ Pages = {93-111},
+ Title = {{Measuring Biodiversity Value for Conservation}},
+ Volume = 26,
+ Year = 1995}
+
+ at article{HNW1999,
+ Author = {Daniel H. Huson and Scott M. Nettles and Tandy J. Warnow},
+ Journal = {Journal of Computational Biology},
+ Pages = {369-386},
+ Title = {Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction},
+ Volume = 6,
+ Year = 1999}
+
+ at article{huson2006,
+ Author = {Huson, Daniel H. and Bryant, David},
+ Doi = {10.1093/molbev/msj030},
+ Journal = {Mol. Biol. Evol.},
+ Keywords = {phylogeny; networks; software; confidence intervals; SplitsTree},
+ Pages = {254-267},
+ Pdf = {huson2006.mbe.pdf},
+ Pmid = {16221896},
+ Title = {Application of Phylogenetic Networks in Evolutionary Studies},
+ Volume = 23,
+ Year = 2006,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msj030}}
+
+ at article{GuohuaJin11012006,
+ Abstract = {Motivation: Horizontal gene transfer (HGT) is believed to be ubiquitous among
+bacteria, and plays a major role in their genome diversification as well as their ability to
+develop resistance to antibiotics. In light of its evolutionary significance and implications for
+human health, developing accurate and efficient methods for detecting and reconstructing HGT is
+imperative. Results: In this article we provide a new HGT-oriented likelihood framework for many
+problems that involve phylogeny-based HGT detection and reconstruction. Beside the formulation of
+various likelihood criteria, we show that most of these problems are NP-hard, and offer heuristics
+for efficient and accurate reconstruction of HGT under these criteria. We implemented our
+heuristics and used them to analyze biological as well as synthetic data. In both cases, our
+criteria and heuristics exhibited very good performance with respect to identifying the correct
+number of HGT events as well as inferring their correct location on the species tree. Availability:
+implementation of the criteria as well as heuristics and hardness proofs are available from the
+authors upon request. Hardness proofs can also be downloaded at
+http://www.cs.tau.ac.il/~tamirtul/MLNET/Supp-ML.pdf Contact: tamirtul at post.tau.ac.il Supplementary
+information: Supplementary data are available at Bioinformatics online.},
+ Author = {Jin, Guohua and Nakhleh, Luay and Snir, Sagi and Tuller, Tamir},
+ Doi = {10.1093/bioinformatics/btl452},
+ Eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/22/21/2604.pdf},
+ Journal = {Bioinformatics},
+ Number = 21,
+ Pages = {2604-2611},
+ Title = {Maximum likelihood of phylogenetic networks},
+ Url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/21/2604},
+ Volume = 22,
+ Year = 2006,
+ Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/21/2604},
+ Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btl452}}
+
+ at article{JhJe2000,
+ Author = {Myoungshic Jhun and Hyeong-Chul Jeong},
+ Journal = {Computational Statistics and Data Analysis},
+ Keyword = {Simultaneous confidence region; Bootstrap; Average coverage probability},
+ Pages = {83-91},
+ Title = {{Applications of Bootstrap Methods for Categorical Data Analysis}},
+ Volume = 35,
+ Year = 2000}
+
+ at article{KaHu1998,
+ Author = {R. Karchin and R. Hughey},
+ Issn = {1367-4803},
+ Journal = {Bioinformatics.},
+ Keywords = {*Algorithms; *{Markov} Chains; Proteins/chemistry; Sequence Analysis/methods; Support, Non-U.S. Gov't; Support, U.S. Gov't, Non-P.H.S.},
+ Language = {english},
+ Number = 9,
+ Pages = {772--782},
+ Title = {Weighting hidden {Markov} models for maximum discrimination},
+ Volume = 14,
+ Year = 1998}
+
+ at article{KBB1990,
+ Author = {S. Karlin and B.~E. Blaisdell and V. Brendel},
+ Issn = {0076-6879},
+ Journal = {Methods.Enzymol.},
+ Keywords = {*Amino Acid Sequence; Animal; *Base Sequence; Codon/genetics; Drosophila/genetics; Escherichia coli/genetics; Heat-Shock Proteins/genetics; Molecular Sequence Data; Proteins/*genetics; *Sequence Homology, Nucleic Acid; Statistics; Support, Non-U.S. Gov't; Support, U.S. Gov't, Non-P.H.S.; Support, U.S. Gov't, P.H.S.},
+ Language = {english},
+ Pages = {388--3402},
+ Title = {{Identification of significant sequence patterns in proteins}},
+ Volume = 183,
+ Year = 1990}
+
+ at article{KaLe1991,
+ Author = {Samuel Karlin and Ming-Ying Leung},
+ Classmath = {60C05;60F05;05A16},
+ Issn = {1050-5164},
+ Journal = {Ann. Appl. Probab.},
+ Language = {English},
+ Number = 4,
+ Pages = {513--538},
+ Title = {Some limit theorems on distributional patterns of balls in urns},
+ Volume = 1,
+ Year = 1991}
+
+ at article{KaBr1992,
+ Author = {S. Karlin and V. Brendel},
+ Journal = {Science},
+ Month = {July},
+ Number = 5066,
+ Pages = {39--49},
+ Title = {Chance and statistical significance in protein and {DNA} sequence analysis},
+ Volume = 257,
+ Year = 1992}
+
+ at article{KaAl1993,
+ Author = {S. Karlin, S. and S.~F. Altschul},
+ Journal = {Proc. Natl. Acad. Sci.},
+ Number = 12,
+ Pages = {5873--5877},
+ Title = {Applications and statistics for multiple high-scoring segments in molecular sequences},
+ Volume = 90,
+ Year = 1993}
+
+ at article{KaCa1994,
+ Author = {S. Karlin and L.~R. Cardon},
+ Journal = {Annu. Rev. Microbiol.},
+ Pages = {619--54},
+ Title = {Computational {DNA} sequence analysis},
+ Volume = 48,
+ Year = 1994}
+
+ at article{KLB1994,
+ Author = {S. Karlin and I. Ladunga and B.~E. Blaisdell},
+ Journal = {Proc. Natl. Acad. Sci.},
+ Number = 26,
+ Pages = {12837--12841},
+ Title = {Heterogeneity of genomes: measures and values},
+ Volume = 91,
+ Year = 1994}
+
+ at article{KaLa1994,
+ Author = {S. Karlin and I. Ladunga},
+ Journal = {Proc. Natl. Acad. Sci.},
+ Number = 26,
+ Pages = {12832--12836},
+ Title = {Comparisons of eukaryotic genomic sequences},
+ Volume = 91,
+ Year = 1994}
+
+ at article{Karl1994,
+ Author = {Samuel Karlin},
+ Journal = {Philos. Trans. R. Soc. Lond. B. Biol. Sci.},
+ Month = Jun,
+ Number = 1310,
+ Pages = {391--402},
+ Title = {Statistical studies of biomolecular sequences: score-based methods},
+ Volume = 344,
+ Year = 1994}
+
+ at article{KCM1998,
+ Author = {S. Karlin and A.~M. Campbell and J. Mrazek},
+ Journal = {Annu Rev Genet},
+ Pages = {185--225},
+ Title = {Comparative {DNA} analysis across diverse genomes},
+ Volume = 32,
+ Year = 1998}
+
+ at article{Kemp1998,
+ Author = {Martin Kemp},
+ Journal = {Nature},
+ Pages = 447,
+ Title = {{Haeckel's Hierarchies}},
+ Volume = 395,
+ Year = 1998}
+
+ at book{King1980,
+ Author = {John~F.C. Kingman},
+ Isbn = {0-898-71166-5},
+ Publisher = {Society for Industrial and Applied Mathematics},
+ Series = {Regional Conference Series in Applied Mathematics},
+ Title = {{Mathematics of Genetic Diversity}},
+ Year = 1980}
+
+ at inproceedings{King1982a,
+ Author = {John~F.C. Kingman},
+ Booktitle = {Essays in Statistical Science},
+ Editor = {J. Gani and E.J. Hannah},
+ Pages = {27-43},
+ Series = {Journal of Applied Probability},
+ Title = {On the Genealogy of Large Populations},
+ Volume = {19A},
+ Year = 1982}
+
+ at phdthesis{Klae2005,
+ Author = {Steffen Kl\"{a}re},
+ Month = {April},
+ School = {Ludwig-Maximilian-Universit\"{a}t Munich},
+ Title = {{Stochastic Models of {Molecular Evolution}: An Algebraical and Statistical Analysis}},
+ Year = 2005}
+
+ at mastersthesis{Klae2000,
+ Author = {Steffen Kl{\"a}re},
+ Language = {german},
+ Month = {October},
+ School = {Friedrich-Schiller-Universit{\"at} Jena},
+ Title = {{\"U}ber ein Klasse stochastischer Differentialgleichungen ohne Adaptiertheitsforderung},
+ Year = 2000}
+
+ at book{Knip1995,
+ Address = {Stuttgart [u.a.]},
+ Author = {Rolf Knippers},
+ Edition = 6,
+ Isbn = {3-13-477006-7},
+ Pages = 508,
+ Publisher = {Thieme},
+ Title = {{Molekulare Genetik}},
+ Year = 1995}
+
+ at article{KnHe1999,
+ Author = {Knudsen, B. and Hein, J.},
+ Issn = {1367-4803},
+ Journal = {Bioinformatics.},
+ Keywords = {Algorithms; Base Sequence; Computational Biology; Computer Simulation; Endoribonucleases/genetics; Evolution; Molecular Sequence Data; *Nucleic Acid Conformation; Probability; RNA/*chemistry; RNA, Bacterial/chemistry/genetics; RNA, Catalytic/genetics; Sequence Homology, Nucleic Acid; Stochastic Processes; Support, Non-U.S. Gov't},
+ Language = {english},
+ Number = 6,
+ Pages = {446--454},
+ Title = {RNA secondary structure prediction using stochastic context-free grammars and {Evolutionary} history},
+ Volume = 15,
+ Year = 1999}
+
+ at article{KCAEJ2000,
+ Author = {Koenigsberger, C. and Chicca JJ, 2nd and Amoureux, M.C. and Edelman, G.M. and Jones, F.S.},
+ Issn = {0027-8424},
+ Journal = {Proc.Natl.Acad.Sci.U.S.A.},
+ Keywords = {Alternative Splicing; Animal; Base Sequence; {DNA}, Complementary; Enhancer Elements (Genetics); Exons; *Gene Expression Regulation; Hela Cells; Human; Mice; Molecular Sequence Data; *Promoter Regions (Genetics); Repressor Proteins/*genetics; RNA, Messenger; Support, Non-U.S. Gov't; Support, U.S. Gov't, Non-P.H.S.; Tumor Cells, Cultured; 3T3 Cells; 5' Untranslated Regions; MHDA- 2000/02/26 09:00},
+ Language = {english},
+ Number = 5,
+ Pages = {2291--2296},
+ Title = {Differential regulation by multiple promoters of the gene encoding the neuron-restrictive silencer factor},
+ Volume = 97,
+ Year = 2000}
+
+ at article{KTG1998,
+ Author = {E.~V. Koonin and R.~L. Tatusov and M.~Y. Galperin},
+ Issn = {0959-440X},
+ Journal = {Curr.Opin.Struct.Biol.},
+ Keywords = {Animal; Bacteria/genetics; Computer Simulation; {DNA}/*chemistry/*genetics; Evolution, Molecular; *Genome; Helicobacter pylori/enzymology/genetics; Human; Models, Genetic; Proteins/chemistry/classification/genetics; Variation (Genetics)},
+ Language = {english},
+ Number = 3,
+ Pages = {355--363},
+ Title = {Beyond complete genomes: from sequence to structure and function},
+ Volume = 8,
+ Year = 1998}
+
+ at article{korostensky2000,
+ Author = {Chantal Korostensky and Gaston~H. Gonnet},
+ Doi = {10.1093/bioinformatics/16.7.619},
+ Journal = {Bioinformatics},
+ Number = 7,
+ Pages = {619-627},
+ Pdf = {korostensky2000.traveling_salesman.bioinformatics.pdf},
+ Title = {Using Traveling Salesman Problem Algorithms for Evolutionary Tree Reconstruction},
+ Volume = 16,
+ Year = 2000,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/16.7.619}}
+
+ at book{KLS1991,
+ Author = {Bernhard Korte and L\'aszl\'o Lov\'asz and Rainer Schrader},
+ Isbn = {0-387-18190-3},
+ Publisher = {Springer Verlag Berlin},
+ Series = {Algorithms and Combinatorics},
+ Title = {Greedoids},
+ Year = 1991}
+
+ at unpublished{KNRV1998,
+ Author = {A. Krause and P. Nicod{\`e}me and M. Rehmsmeier and M. Vingron},
+ Note = {Lecture at GCB'98},
+ Title = {{Automatic clustering of large sequence databases}},
+ Year = 1998}
+
+ at article{KrVi1998,
+ Author = {A. Krause and M. Vingron},
+ Issn = {1367-4803},
+ Journal = {Bioinformatics.},
+ Keywords = {Algorithms; Cluster Analysis; Comparative Study; Computational Biology; *Databases, Factual; Proteins/*genetics; Sequence Alignment/*methods/statistics & numerical data; Software; Support, Non-U.S. Gov't},
+ Language = {english},
+ Number = 5,
+ Pages = {430--438},
+ Title = {A set-theoretic approach to database searching and clustering},
+ Volume = 14,
+ Year = 1998}
+
+ at misc{KM2004,
+ Author = {Peter Kwok and Charles Matthews},
+ Title = {Greedoid},
+ Url = {http://en.wikipedia.org/wiki/Greedoid},
+ Year = 2004,
+ Bdsk-Url-1 = {http://en.wikipedia.org/wiki/Greedoid}}
+
+ at article{Lake1997,
+ Author = {James~A. Lake},
+ Journal = {Molecular Biology and Evolution},
+ Number = 3,
+ Pages = {213-219},
+ Title = {{Phylogenetic Inference: How Much Evolutionary History is Knowable?}},
+ Volume = 14,
+ Year = 1997}
+
+ at article{lanfear2012,
+ Author = {Lanfear, Robert and Calcott, Brett and Ho, Simon Y. W. and Guindon, Stephane},
+ Doi = {10.1093/molbev/mss020},
+ Journal = {Mol. Biol. Evol.},
+ Keywords = {model selection; evolutionary models; alignment partitioning;; partitioning; AIC; BIC; AICc; model selection; molecular evolution},
+ Pages = {1695-1701},
+ Paperurl = {http://mbe.oxfordjournals.org/content/29/6/1695},
+ Pdf = {lanfear2012.mbe.pdf},
+ Pmid = {22319168},
+ Project = {journal-club; JC},
+ Source = {http://www.robertlanfear.com/partitionfinder},
+ Title = {{PartitionFinder}: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses},
+ Volume = 29,
+ Year = 2012,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/mss020}}
+
+ at book{Lang1997,
+ Address = {New York},
+ Author = {Kenneth Lange},
+ Isbn = {0-387-94909-7},
+ Publisher = {Springer},
+ Series = {Statistics for Biology and Health},
+ Title = {{Mathematical and statistical methods for genetic analysis}},
+ Year = 1997}
+
+ at book{Laur1996,
+ Address = {Oxford},
+ Author = {Steffen L. Lauritzen},
+ Isbn = {0-19-852219-3},
+ Pages = 298,
+ Publisher = {Clarendon Press},
+ Series = {Oxford Stastical Science Series},
+ Title = {Graphical Models},
+ Year = 1996}
+
+ at inproceedings{Laur2001,
+ Author = {Steffen L. Lauritzen},
+ Booktitle = {Complex Stochastic Systems},
+ Pages = {63-107},
+ Publisher = {Chapman \& Hall, London, Boca Raton},
+ Sereditor = {O.~E. Barndorff-Nielsen and D.~R. Cox and C. Kl{\"u}ppelberg},
+ Title = {Causal inference from graphical models},
+ Year = 2001}
+
+ at book{lawler1998,
+ Address = {Boston},
+ Author = {Lawler, Gregory F.},
+ Isbn = {0-81-763892-X},
+ Pages = 230,
+ Publisher = {Birkh{\"a}user},
+ Series = {Probability and its Applications},
+ Title = {Intersections of Random Walks},
+ Year = 1998}
+
+ at incollection{Laza1966,
+ Author = {Paul F. Lazarfeld},
+ Booktitle = {Measurement and Prediction},
+ Chapter = 10,
+ Isbn = {0-844-63021-7},
+ Pages = {362-412},
+ Publisher = {Wiley, New York},
+ Title = {{Latent Structure Analysis}},
+ Year = 1966}
+
+ at article{LNS2002,
+ Author = {Alan~J. Lee and Stephen~O. Nyangoma and George~A.F. Seber},
+ Journal = {Computational Statistics and Data Analysis},
+ Keywords = {Confidence regions; Coverage; Curvature; Likelihood ratio test; {Multinomial} Distribution; Pearson $\chi^2$ test; Score test},
+ Pages = {329-342},
+ Title = {{Confidence Regions for {Multinomial} Parameters}},
+ Volume = 39,
+ Year = 2002}
+
+ at article{levy2006,
+ Author = {Levy, Dan and Yoshida, Ruriko and Pachter, Lior},
+ Doi = {10.1093/molbev/msj059},
+ Journal = {Mol. Biol. Evol.},
+ Keywords = {neighbor-joining; phylogenetic diversity; subtree weights; mjoin},
+ Pages = {491-498},
+ Pdf = {levy2006.mbe.pdf},
+ Pmid = {16280538},
+ Source = {http://bio.math.berkeley.edu/mjoin/},
+ Title = {Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates},
+ Volume = 23,
+ Year = 2006,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msj059}}
+
+ at article{lewis2003,
+ Author = {Paul~O. Lewis},
+ Journal = {Bioinformatics},
+ Number = 17,
+ Pages = {2330-2331},
+ Title = {{NCL}: a {C++} class library for interpreting data files in {NEXUS} format},
+ Volume = 19,
+ Year = 2003}
+
+ at article{lewis2005,
+ Author = {Louise~A. Lewis and Paul~O. Lewis},
+ Issn = {1063-5157},
+ Journal = {Syst. Biol.},
+ Number = 6,
+ Pages = {936-947},
+ Title = {Unearthing the Molecular Diversity of Desert Soil Green Algae},
+ Volume = 54,
+ Year = 2005}
+
+ at article{LePo1997,
+ Author = {Mohamed Lemdani and Odile Pons},
+ Classmath = {62P10;62F05;92D10},
+ Issn = {0167-7152},
+ Journal = {Stat. Probab. Lett.},
+ Keywords = {{Binomial} mixture; homogeneity; likelihood ratio tests; linkage},
+ Language = {English},
+ Number = 1,
+ Pages = {15-22},
+ Title = {Likelihood ratio tests for genetic linkage},
+ Volume = 33,
+ Year = 1997}
+
+ at article{LA1995,
+ Author = {Peter Lescia and Fred~W. Allendorf},
+ Journal = {Conservation Biology},
+ Number = 4,
+ Pages = 753,
+ Title = {{When Are Peripheral Populations Valuable for Conservation?}},
+ Volume = 6,
+ Year = 1995}
+
+ at article{LYP2006,
+ Author = {Dan Levy and Ruriko Yoshida and Lior Pachter},
+ Journal = {Mol. Biol. Evol.},
+ Pages = {491-498},
+ Title = {{Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity}},
+ Volume = 23,
+ Year = 2006}
+
+ at book{Lewi1997,
+ Address = {Oxford etc.},
+ Author = {Benjamin Lewin},
+ Edition = 6,
+ Isbn = {0-19-857778-8},
+ Publisher = {Oxford Univ. Press},
+ Title = {Genes},
+ Year = 1997}
+
+ at article{Lewi1988,
+ Author = {Robert Lewin},
+ Journal = {Science},
+ Month = {April},
+ Number = 4852,
+ Pages = 603,
+ Title = {{Chance and Repetition}},
+ Volume = 240,
+ Year = 1988}
+
+ at article{LiLa1999,
+ Author = {Liu, Jun S. and Lawrence, Charles E.},
+ Journal = {Bioinformatics},
+ Number = 1,
+ Pages = {38--52},
+ Title = {{Bayesian} Inference on biopolymer models},
+ Volume = 15,
+ Year = 1999}
+
+ at article{maddison1997,
+ Author = {Maddison, David R. and Swofford, David L. and Maddison, Wayne P.},
+ Journal = {Syst. Biol.},
+ Keywords = {Computer program; file format; NEXUS; systematics},
+ Pages = {590-621},
+ Pdf = {maddison1997.syst-biol.pdf},
+ Title = {{NEXUS}: An Extensible File Format for Systematic Information},
+ Volume = 46,
+ Year = 1997}
+
+ at article{MGP2003,
+ Author = {Georgina~M. Mace and John~L. Gittleman and Andy Purvis},
+ Journal = {Science},
+ Pages = {1707-1709},
+ Title = {{Preserving the Tree of Life}},
+ Volume = 300,
+ Year = 2003}
+
+ at article{MaPe2004,
+ Author = {Thomas Mailund and Christian N.~S. Pederson},
+ Journal = {Bioinformatics},
+ Keywords = {Neighbour-Joining},
+ Number = 17,
+ Pages = {3261-3262},
+ Title = {{QuickJoin - Fast Neighbour-Joining Tree Reconstruction}},
+ Volume = 20,
+ Year = 2004}
+
+ at article{margules1988,
+ Author = {Margules, C. R. and Nicholls, A. O. and Pressey, R. L.},
+ Doi = {10.1016/0006-3207(88)90078-X},
+ Journal = {Biol. Conserv.},
+ Pages = {63-76},
+ Pdf = {margules1988.biol-conserv.pdf},
+ Title = {Selecting Networks of Reserves to Maximise Biological Diversity},
+ Volume = 43,
+ Year = 1988,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1016/0006-3207(88)90078-X}}
+
+ at article{Matu1992,
+ Author = {Frantisek Mat\'{u}s},
+ Journal = {Journal of Applied Probability},
+ Pages = {745-749},
+ Title = {On Equivalence of {Markov} Properties over Undirected Graphs},
+ Volume = 29,
+ Year = 1992}
+
+ at article{mascagni2000,
+ Author = {Mascagni, M and Srinivasan, A},
+ Journal = {ACM Transactions on Mathematical Software},
+ Pages = {436-461},
+ Title = {Algorithm 806: {SPRNG}: A scalable library for pseudorandom number generation},
+ Volume = 26,
+ Year = 2000}
+
+ at article{MaJo1997,
+ Author = {Warren~L. May and William~D. Johnson},
+ Journal = {Communications in Statistics},
+ Keywords = {categorial data; {Multinomial} distribution; simultaneous interval estimation; accuracy of confidence statement},
+ Number = 2,
+ Pages = {495-518},
+ Title = {{Properties of Simultaneous Confidence Intervals for {Multinomial} Proportions}},
+ Volume = 26,
+ Year = 1997}
+
+ at article{McAA1997,
+ Author = {McAdams, H.H. and Arkin, A.},
+ Issn = {0027-8424},
+ Journal = {Proc.Natl.Acad.Sci.U.S.A.},
+ Keywords = {Algorithms; Computer Simulation; Gene Expression Regulation/*physiology; *Models, Genetic; Proteins/genetics; Stochastic Processes; Support, U.S. Gov't, Non-P.H.S.; Transcription, Genetic; Translation, Genetic},
+ Language = {english},
+ Number = 3,
+ Pages = {814--819},
+ Title = {Stochastic mechanisms in gene expression},
+ Volume = 94,
+ Year = 1997}
+
+ at article{MeDu2004,
+ Author = {Julien Meunier and Laurent Duret},
+ Journal = {Mol. Biol. Evol.},
+ Keywords = {GC-Content},
+ Month = {February},
+ Number = 6,
+ Pages = {984-990},
+ Source = {{\tt http://mbe.oup JOURNALs.org/cgi/content/ abstract/21/6/984}},
+ Title = {{Recombination Drives the Evolution of {GC}-Content in the Human Genome}},
+ Volume = 21,
+ Year = 2004}
+
+ at article{minh2005a,
+ Author = {Minh, Bui Quang and Vinh, Le Sy and von Haeseler, Arndt and Schmidt, Heiko A.},
+ Doi = {10.1093/bioinformatics/bti594},
+ Journal = {Bioinformatics},
+ Keywords = {parallel computing; parallel bioinformatics;; reconstruction of large phylogenies; maximum likelihood (ML); MPI; pIQPNNI},
+ Pages = {3794-3796},
+ Pdf = {minh2005a.bioinformatics.pdf},
+ Pmid = {16046495},
+ Title = {{pIQPNNI} -- parallel reconstruction of large maximum likelihood phylogenies},
+ Volume = 21,
+ Year = 2005,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/bti594}}
+
+ at article{minh2009,
+ Author = {Minh, Bui Quang and Pardi, Fabio and Klaere, Steffen and von Haeseler, Arndt},
+ Doi = {10.1109/TCBB.2008.54},
+ Journal = {IEEE/ACM Trans. Comput. Biol. Bioinform.},
+ Keywords = {Biodiversity conservation; phylogenetic diversity; budget constraint; dynamic programming; phylogenetic network; split system},
+ Pages = {22-29},
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+ Year = 2003}
+
+ at article{YaSp2005,
+ Author = {Von Bing Yap and Terry Speed},
+ Journal = {BMC {Evolutionary} Biology},
+ Month = {January},
+ Note = {{\tt http://www.biomedcentral.com/1471-2148/5/2}},
+ Number = 2,
+ Title = {{Rooting a phylogenetic tree with nonreversible substitution models}},
+ Volume = 5,
+ Year = 2005}
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+ at article{yule1925,
+ Author = {Yule, G. Udny},
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+ Keywords = {Theory of Evolution; Birth-Process},
+ Pages = {21-87},
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+ Title = {A Mathematical Theory of Evolution, Based on the Conclusions of {Dr. J. C. Willis, F.R.S.}},
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+ Language = {english},
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+ Issn = {0305-1048},
+ Journal = {Nucleic.Acids.Res.},
+ Keywords = {Adenosinetriphosphatase; *Algorithms; *Amino Acid Sequence; Archaeal Proteins; Calcium-Binding Proteins; Comparative Study; Databases, Factual; {DNA} Primase; Heat-Shock Proteins 90; Helminth Proteins; *Pattern Recognition; RNA Nucleotidyltransferases; *Software},
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+ Keywords = {Animal; Chromatids/*genetics; Chromosomes/genetics; Chromosomes, Human/genetics; *Crossing Over (Genetics); Drosophila melanogaster/*genetics; Female; Human; *Likelihood Functions; Male; *Models, Genetic; Sister Chromatid Exchange; Support, Non-U.S. Gov't; Support, U.S. Gov't, Non-P.H.S.; X Chromosome/genetics},
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+ at article{guindon2010,
+ Abstract = {PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696--704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and [...]
+ Author = {Guindon, St{\'e}phane and Dufayard, Jean-Fran{\c c}ois and Lefort, Vincent and Anisimova, Maria and Hordijk, Wim and Gascuel, Olivier},
+ Doi = {10.1093/sysbio/syq010},
+ Eprint = {http://sysbio.oxfordjournals.org/content/59/3/307.full.pdf+html},
+ Journal = {Syst. Biol.},
+ Number = {3},
+ Pages = {307-321},
+ Title = {New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0},
+ Url = {http://sysbio.oxfordjournals.org/content/59/3/307.abstract},
+ Volume = {59},
+ Year = {2010},
+ Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/59/3/307.abstract},
+ Bdsk-Url-2 = {http://dx.doi.org/10.1093/sysbio/syq010}}
diff --git a/debian/Documents_source/heiko.bib b/debian/Documents_source/heiko.bib
new file mode 100644
index 0000000..99f976b
--- /dev/null
+++ b/debian/Documents_source/heiko.bib
@@ -0,0 +1,27235 @@
+
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+ KEYWORDS = {}
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+ PDF = {adachi1996.jme.pdf},
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+ }
+
+ at ARTICLE{adachi1996a,
+ AUTHOR = {Adachi, Jun and Hasegawa, Masami},
+ YEAR = 1996,
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+ KEYWORDS = {Maximum likelihood; General reversible Markov model; Amino acid substitution; Chloroplast DNA; AA LogDet}
+ }
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+ MONTH = {September},
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+ SCHOOL = {Department of Computing Imperial College},
+ TYPE = {Master's thesis},
+ ADRESS = {London, UK},
+ PDF = {afzal2004.mastersthesis.pdf},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {parallel computing; scheduling; SGE; Sun Grid Engine; Advanced Reservation Support}
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+ PAGES = {255-266},
+ PDF = {alfaro2003.mbe.pdf},
+ DOI = {10.1093/molbev/msg028},
+ PMID = {12598693},
+ KEYWORDS = {Bayesian Markov chain Monte Carlo; bootstrap; maximum parsimony; maximum likelihood; posterior probability; phylogenetic confidence; simulation}
+ }
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+ KEYWORDS = {trees; metrics; subtree transfer; fixed parameter tractability;; tree distance}
+ }
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+ PDF = {altekar2004.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg427},
+ PMID = {14960467},
+ KEYWORDS = {parallel computing; parallel bioinformatics;; MCMCMC; MrBayes; Bayesian analysis}
+ }
+
+ at ARTICLE{altschul1990,
+ AUTHOR = {Altschul, Stephen F. and Gish, Warren and Miller, Webb and Myers, Eugene W. and Lipman, David J.},
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+ KEYWORDS = {parallel computing; parallel random number generator}
+ }
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+ at ARTICLE{aluru2003,
+ AUTHOR = {Aluru, Srinivas and Futamura, Natsuhiko and Mehrotra, Kishan},
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+ PDF = {aluru2003.jpdc.pdf},
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+ }
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+ at ARTICLE{alvarez1998,
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+ TITLE = {Eukaryotic diversity in {Spain's} {River of Fire}},
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+ AUTHOR = {Amdahl, Gene M.},
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+ }
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+ AUTHOR = {Amrine, Heather M. and Springer, Mark S.},
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+ TITLE = {Maximum-Likelihood Analysis of the {Tethythere} Hypothesis Based on a Multigene Data Set and a Comparison of Different Models of Sequence Evolution},
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+ PAGES = {161-176},
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+ KEYWORDS = {Tethytheria; Sirenia; Proboscidea; Hyracoidea; maximum likelihood; mutiple genes}
+ }
+
+ at ARTICLE{amrine2003,
+ AUTHOR = {Amrine, Heather M. and Scally, Mark and Westerman, Michael and Stanhope, Michael J. and Krajewski, Carey and Springer, Mark S.},
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+ TITLE = {Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials},
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+ PDF = {amrine2003.mpe.pdf},
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+ KEYWORDS = {monophyly of australidelphian marsupials; mammalia}
+ }
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+ }
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+ AUTHOR = {Anderson, Jon P. and Rodrigo, Allen G. and Learn, Gerald H. and Wang, Yang and Weinstock, Hillard and Kalish, Marcia L. and Robbins, Kenneth E. and Hood, Leroy and Mullins, James I.},
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+ }
+
+ at ARTICLE{anderson2001a,
+ AUTHOR = {Anderson, Jason S.},
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+ }
+
+ at ARTICLE{anderson2002,
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+ KEYWORDS = {parallel bioinformatics; parallel computing; high-performance computing; computational genomics; phylogeny reconstruction; breakpoint analysis; gene rear-rangement; drug discovery}
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+ at ARTICLE{baeck1993,
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+ at ARTICLE{baldauf2002,
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+ YEAR = 2002,
+ TITLE = {The tree of life is a tree (more or less)},
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+ at ARTICLE{baldauf2003,
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+ at ARTICLE{baldauf2003a,
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+
+ at ARTICLE{ballard1992,
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+ at ARTICLE{bandelt1999,
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+ at ARTICLE{barker2004,
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+ AUTHOR = {Barthelemy, J. P. and Guenoche, A.},
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+ DOI = {10.1007/s002240010013},
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+ KEYWORDS = {parallel computing; task scheduling}
+ }
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+ at ARTICLE{bastien2004,
+ AUTHOR = {Bastien, Olivier and Aude, Jean-Christophe and Roy, Sylvaine and Mar{\'e}chal, Eric},
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+ DOI = {10.1093/bioinformatics/btg440},
+ PMID = {14751978},
+ REMARK = {14990449 (BI) or 14751978 (PubMed) ??},
+ KEYWORDS = {pairwise alignments; protein sequences; theoretical significance; Z-score statistics}
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+ at ARTICLE{bataillon2003,
+ AUTHOR = {Bataillon, Thomas},
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+ TITLE = {Shaking the 'deleterious mutations' dogma?},
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+ PDF = {bataillon2003.tree.pdf},
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+ PMID = {},
+ KEYWORDS = {deleterious mutations}
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+ at ARTICLE{battaglia2000,
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+ at ARTICLE{bauer2002,
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+ TITLE = {Genetic Algorithms and Parallel Processing in Maximum-Likelihood Phylogeny Inference},
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+ PAGES = {1717-1726},
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+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing; genetic algorithm; phylogeny inference; maximum likelihood; parallel algorithm; nucleotide sequence data}
+ }
+
+ at ARTICLE{baum1992,
+ AUTHOR = {Baum, Bernard R.},
+ YEAR = 1992,
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+ at ARTICLE{baum1993,
+ AUTHOR = {Baum, Bernard R. and Ragan, Mark A.},
+ YEAR = 1993,
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+ PDF = {hardcopy},
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+ KEYWORDS = {combining phylogenetic trees; supertree}
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+ at ARTICLE{bafna2003,
+ AUTHOR = {Bafna, Vineet and Gusfield, Dan and Lancia, Giuseppe and Yooseph, Shibu},
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+ KEYWORDS = {algorithms, haplotypes, phasing, perfect phylogeny}
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+
+ at BOOK{baxevanis2002,
+ EDITOR = {Baxevanis, Andreas D. and Davison, Daniel B. and Page, Roderic D. M. and Stormo, Gary and Stein, Lincoln},
+ YEAR = 2002,
+ TITLE = {Current Protocols in Bioinformatics},
+ PUBLISHER = {Wiley and Sons},
+ ADDRESS = {New York, USA},
+ ISBN = {0-471-25093-7},
+ KEYWORDS = {Bioinformatics}
+ }
+
+ at ARTICLE{baxevanis2003,
+ AUTHOR = {Baxevanis, Andreas D.},
+ YEAR = 2003,
+ TITLE = {The Molecular Biology Database Collection: 2003 update},
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+ PAGES = {1-12},
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+ DOI = {10.1093/nar/gkg120},
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+ KEYWORDS = {Molecular Biology Databases}
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+ PDF = {bayley1998.jme.pdf},
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+ at ARTICLE{beaumont2003,
+ AUTHOR = {Beaumont, Olivier and Legrand, Arnaud and Robert, Yves},
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+ DOI = {10.1016/S0167-8191(03)00095-4},
+ PMID = {-},
+ KEYWORDS = {parallel computing; scheduling;; Scheduling; Divisible tasks; Multi-round algorithms; Asymptotical optimality}
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+ at ARTICLE{bejerano2001,
+ AUTHOR = {Bejerano, Gill and Seldin, Yevgeny and Margalit, Hanah and Tishby, Naftali},
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+ JOURNAL = {Bioinformatics},
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+ PDF = {bejerano2001.bioinformatics.pdf},
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+ KEYWORDS = {pairwise sequence alignment; bioinformatics; gap penalties}
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+
+ at ARTICLE{bellis1994,
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+ AUTHOR = {Benabib, Miriam and Kjer, Karl M. and Sites, Jr., Jack W.},
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+ TITLE = {Mitochondrial {DNA} Sequence-Based Phylogeny and the Evolution of Viviparity in the {Sceloporus scalaris} Group ({Reptilia}, {Squamata})},
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+ PAGES = {1262-1275},
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+ at ARTICLE{bendor1998,
+ AUTHOR = {Ben-dor, Amir and Chor, Benny and Graur, Dan and Ophir Ron and Pelleg, Dan},
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+
+ at INPROCEEDINGS{bendor1998a,
+ AUTHOR = {Ben-dor, Amir and Chor, Benny and Graur, Dan and Ophir Ron and Pelleg, Dan},
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+ TITLE = {From four-taxon trees to phylogenies (preliminary report): the case of mammalian evolution},
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+ MONTH = {},
+ PUBLISHER = {ACM Press},
+ ADDRESS = {New York, USA},
+ PDF = {bendor1998a.RECOMB.pdf},
+ DOI = {10.1145/279069.279078},
+ PMID = {},
+ KEYWORDS = {quartet method; phylogeny reconstruction; mammalian evolution}
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+ at ARTICLE{bengtson1998,
+ AUTHOR = {Bengtson, Stefan},
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+ TITLE = {{GenBank}},
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+
+ at ARTICLE{benson2002,
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+ TITLE = {{GenBank}},
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+ AUTHOR = {Benson, Dennis A. and Karsch-Mizrachi, Ilene and Lipman, David J. and Ostell, James and Wheeler, David L.},
+ YEAR = 2003,
+ TITLE = {{GenBank}},
+ JOURNAL = {Nucleic Acids Res.},
+ VOLUME = 31,
+ PAGES = {23-27},
+ PDF = {benson2003.nar.pdf},
+ DOI = {10.1093/nar/gkg057},
+ PMID = {12519940},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{benton1995,
+ AUTHOR = {Benton, Michael J.},
+ YEAR = 1995,
+ TITLE = {Testing the Time Axis of Phylogenies},
+ JOURNAL = {Philos. Trans. R. Soc. Lond. Ser. B},
+ VOLUME = 349,
+ PAGES = {5-10},
+ PDF = {benton1995.phil-trans-rsoc-b.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {testing phylogeny; time axis}
+ }
+
+ at ARTICLE{benton2003,
+ AUTHOR = {Benton, Michael J.},
+ YEAR = 2003,
+ TITLE = {Dating the Tree of Life},
+ JOURNAL = {Science},
+ VOLUME = 300,
+ PAGES = {1698-1700},
+ PDF = {benton2003.science.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Tree of Life; dating; Underestimating/Overestimating Dates}
+ }
+
+ at ARTICLE{beran1986,
+ AUTHOR = {Beran, Rudolf},
+ YEAR = 1986,
+ TITLE = {Discussion: Jackknife, Bootstrap and Other Resampling Methods in Regression Analysis},
+ JOURNAL = {Ann. Stat.},
+ VOLUME = 14,
+ PAGES = {1295-1298},
+ PDF = {beran1986.ann-stat.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at TECHREPORT{berger2003,
+ AUTHOR = {Berger-Wolf, Tanya Y. and Williams, Tiffani L. and Moret, Bernard E. and Warnow, Tandy J.},
+ YEAR = 2003,
+ TITLE = {An Experimental Evaluation of Phylogenetic Consensus Methods},
+ INSTITUTION = {University New Mexico},
+ ADDRESS = {Albuquerque, NM, USA},
+ TYPE = {UNM Computer Science Tech-Reports},
+ NUMBER = {TR-CS-2003-19},
+ PDF = {berger2003.TR-CS-2003-19.ps.gz},
+ KEYWORDS = {supertree;; Experimental Evaluation; Consensus Methods; supertrees}
+ }
+
+ at TECHREPORT{berger2003a,
+ AUTHOR = {Berger-Wolf, Tanya Y. and Warnow, Tandy J.},
+ YEAR = 2003,
+ TITLE = {Online Consensus of Phylogenetic Trees},
+ INSTITUTION = {University New Mexico},
+ ADDRESS = {Albuquerque, NM, USA},
+ TYPE = {UNM Computer Science Tech-Reports},
+ NUMBER = {TR-CS-2003-34},
+ PDF = {berger2003a.TR-CS-2003-34.ps.gz},
+ KEYWORDS = {Consensus trees;; }
+ }
+
+ at ARTICLE{berry1996,
+ AUTHOR = {Berry, Vincent and Gascuel, Olivier},
+ YEAR = 1996,
+ TITLE = {On the Interpretation of Bootstrap Trees: Appropriate Threshold of Clade Selection and Induced Gain},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 13,
+ PAGES = {999-1011},
+ PDF = {berry1996.mbe.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {bootstrap method; threshold of clade selection; topological distance; Type I and Type II error; bias/variance compromise; maximum parsimony; neighbor joining; computer simulations}
+ }
+
+ at INPROCEEDINGS{berry1999,
+ AUTHOR = {Berry, Vincent and Bryant, David},
+ YEAR = 1999,
+ TITLE = {Faster reliable phylogenetic analysis},
+ BOOKTITLE = {Proceedings of the third annual international conference on Computational molecular biology (RECOMB 1999)},
+ PAGES = {59-68},
+ MONTH = {April},
+ PUBLISHER = {ACM Press},
+ ADDRESS = {New York)},
+ PDF = {berry1999.RECOMB.pdf},
+ DOI = {10.1145/299432.299457},
+ PMID = {},
+ KEYWORDS = {computational biology; phylogeny reconstruction; combinatorially reliable edges; distance based methods; quartet based methods; single linkage tree; polynomial time algorithms; Fast methods; reliability; phylogenetic analysis}
+ }
+
+ at INPROCEEDINGS{berry1999a,
+ AUTHOR = {Berry, Vincent and Jiang, Tao and Kearney, Paul and Li, Ming and Wareham, Todd},
+ YEAR = 1999,
+ TITLE = {Quartet cleaning: Improved algorithms and simulations},
+ BOOKTITLE = {Proceedings of the European Syposium on Algorithms (ESA 1999)},
+ PAGES = {},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{berry2000,
+ AUTHOR = {Berry, Vincent and Gascuel, Olivier},
+ YEAR = 2000,
+ TITLE = {Inferring evolutionary trees with strong combinatorial evidence},
+ JOURNAL = {Theor. Comput. Sci.},
+ VOLUME = 240,
+ PAGES = {271-298},
+ PDF = {berry2000.theor-comput-sci.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Phylogeny reconstruction; Quartet method; Exact polynomial algorithm; Partially resolved tree; Combinatorial technique; Worst-case convergence rate; Experimental study}
+ }
+
+ at ARTICLE{berry2000a,
+ AUTHOR = {Berry, V. and Gascuel, O. and Caraux, G.},
+ YEAR = 2000,
+ TITLE = {Choosing the tree which actually best explains the data: Another look at the bootstrap in phylogenetic reconstruction},
+ JOURNAL = {Comput. Stat. Data Anal.},
+ VOLUME = 32,
+ PAGES = {273-283},
+ PDF = {berry2000a.comput-stat-data-anal.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Phylogeny reconstruction; Tree estimation; Overfitting; Complexity/goodness-of-fit; Bootstrap resampling methods; Cross validation; Structural distance; Four-point condition; Quartets}
+ }
+
+ at INPROCEEDINGS{berry2000b,
+ AUTHOR = {Berry, Vincent and Bryant, David and Jiang, Tao and Kearney, Paul and Li, Ming and Wareham, Todd and Zhang, Haoyong},
+ YEAR = 2000,
+ TITLE = {A practical algorithm for recovering the best supported edges of an evolutionary tree (extended abstract)},
+ BOOKTITLE = {Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms (SODA 2000)},
+ PAGES = {287-296},
+ MONTH = {January},
+ PUBLISHER = {ACM Press},
+ ADDRESS = {New York, USA},
+ PDF = {berry2000b.SODA.pdf},
+ DOI = {10.1145/338219.338265},
+ PMID = {},
+ KEYWORDS = {large datasets; phylogeny reconstruction; hypercleaning method; quartet method; a quartet cleaning method}
+ }
+
+ at ARTICLE{bhaduri2004,
+ AUTHOR = {Bhaduri, Anirban and Pugalenthi, Ganesan and Sowdhamini, Ramanathan},
+ YEAR = 2004,
+ TITLE = {PASS2: an automated database of protein alignments organised as structural superfamilies},
+ JOURNAL = {BMC Bioinformatics},
+ VOLUME = 5,
+ PAGES = {35},
+ PDF = {bhaduri2004.bmc-bioinformatics-manuscript.pdf},
+ DOI = {},
+ PMID = {15059245},
+ KEYWORDS = {protein alignments; structural superfamilies; database}
+ }
+
+ at ARTICLE{bhattacharya1991,
+ AUTHOR = {Bhattacharya, Debashish and Stickel, Shawn K. and Sogin, Mitchell L.},
+ YEAR = 1991,
+ TITLE = {Molecular Phylogenetic Analysis of Actin Genic Regions from {Achlya bisexualis} ({Oomycota}) and {Costaria costata} ({Chromophyta})},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = {33},
+ PAGES = {535-536},
+ PDF = {NICHT VORHANDEN},
+ DOI = {},
+ PMID = {1779434},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{bhattacharya1993,
+ AUTHOR = {Bhattacharya, Debashish and Stickel, Shawn K. and Sogin, Mitchell L.},
+ YEAR = 1993,
+ TITLE = {Isolation and Molecular Phylogenetic Analysis of Actin--coding Region from {E}miliania huxleyi, a Prymnesiophyte Alga by reverse Transcriptase and {PCR}--Methods},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = {10},
+ PAGES = {689-703},
+ PDF = {bhattacharya1993.mbe.pdf},
+ DOI = {},
+ PMID = {7687735},
+ KEYWORDS = {actin; evolution; phylogeny; Emiliania huxleyi}
+ }
+
+ at ARTICLE{bhattacharya1994,
+ AUTHOR = {Bhattacharya, Debashish and Surek, Barbara and R{\"u}sing, Matthias and Dammberger, Simon and Melkonian, Michael},
+ YEAR = 1994,
+ TITLE = {Group {I} introns are inherited through common ancestry in the nuclear-encoded {rRNA} of {Z}ygnematales ({C}harophyceae)},
+ JOURNAL = {Proc. Natl. Acad. Sci. USA},
+ VOLUME = 91,
+ PAGES = {9916-9920},
+ PDF = {bhattacharya1994.pnas.pdf},
+ DOI = {},
+ PMID = {7937917},
+ KEYWORDS = {green algae; lateral transfer; phylogeny; secondary structure}
+ }
+
+ at ARTICLE{bhattacharya1995,
+ AUTHOR = {Bhattacharya, Debashish and Helmchen, Thomas and Bibeau, Claude and Melkonian, Michael},
+ YEAR = 1995,
+ TITLE = {Comparisons of nuclear-encoded small-subunit ribosomal {RNAs} reveal the evolutionary position of the {G}laucocystophyta},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 12,
+ PAGES = {415-420},
+ PDF = {bhattacharya1995.mbe.pdf},
+ DOI = {},
+ PMID = {7739383},
+ KEYWORDS = {cyanelle; Cyanophora paradoxa; Glaucocystophyta; molecular evolution; phylogeny; small-subunit ribosomal RNA; SSU rRNA}
+ }
+
+ at ARTICLE{bhattacharya1995a,
+ AUTHOR = {Bhattacharya, Debashish and Medlin, Linda},
+ YEAR = 1995,
+ TITLE = {The phylogeny of plastids: A review based on comparisons of small subunit ribosomal {RNA} coding regions},
+ JOURNAL = {J. Phycol.},
+ VOLUME = 31,
+ PAGES = {489-498},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{bhattacharya1995b,
+ AUTHOR = {Bhattacharya, Debashish and Ehlting, J{\"u}rgen},
+ YEAR = 1995,
+ TITLE = {Actin Coding Regions: Gene Family Evolution and Use as a Phylogenetic Marker},
+ JOURNAL = {Arch. Protistenkd.},
+ VOLUME = {145},
+ PAGES = {155-164},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Actin; Evolution; Gene family; Phylogeny; Protists}
+ }
+
+ at ARTICLE{bhattacharya1996,
+ AUTHOR = {Bhattacharya, Debashish},
+ YEAR = 1996,
+ TITLE = {Analysis of the Distribution of Bootstrap Tree Lengths Using the Maximum Parsimony Method},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 6,
+ PAGES = {339-350},
+ PDF = {bhattacharya1996.mpe.pdf},
+ DOI = {10.1006/mpev.1996.0084},
+ PMID = {8975690},
+ KEYWORDS = {-}
+ }
+
+ at ARTICLE{bhattacharya1996a,
+ AUTHOR = {Bhattacharya, Debashish and Damberger, Simon and Surek, Barbara and Melkonian, Michael},
+ YEAR = 1996,
+ TITLE = {Primary and secondary structure analyses of the {rRNA} group--{I} introns of the Zygnematales (Charophyta)},
+ JOURNAL = {Curr. Genet.},
+ VOLUME = 29,
+ PAGES = {282-286},
+ PDF = {bhattacharya1996a.curr-genet.pdf},
+ DOI = {},
+ PMID = {8595675},
+ KEYWORDS = {Group-I introns; Secondary structure; Small subunit ribosomal DNA; Zygnematales}
+ }
+
+ at ARTICLE{bhattacharya1996b,
+ AUTHOR = {Bhattacharya, Debashish and Friedl, Thomas and Damberger, Simon},
+ YEAR = 1996,
+ TITLE = {Nuclear--Encoded {rDNA} Group {I} Introns: Origin and Phylogenic Relationships of Insertion Site Lineages in the Green Algae},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 13,
+ PAGES = {978-989},
+ PDF = {bhattacharya1996b.mbe.pdf},
+ DOI = {},
+ PMID = {8752006},
+ KEYWORDS = {green algae; group I introns; lateral transfer; lichens; molecular evolution; phylogeny; secondary structure; small subunit ribosomal DNA}
+ }
+
+ at BOOK{bhattacharya1997,
+ AUTHOR = {Bhattacharya, Debashish},
+ YEAR = 1997,
+ TITLE = {The Origin of Algae an their Plastids},
+ PUBLISHER = {Springer},
+ ADDRESS = {Wien}
+ }
+
+ at INCOLLECTION{bhattacharya1997a,
+ AUTHOR = {Bhattacharya, Debashish and Schmidt, Heiko},
+ TITLE = {Division {G}laucocystophyta},
+ YEAR = 1997,
+ PAGES = {139-148},
+ EDITOR = {Bhattacharya, Debashish},
+ BOOKTITLE = {The Origin of Algae an their Plastids},
+ PUBLISHER = {Springer},
+ ADDRESS = {Wien},
+ CROSSREF = {bhattacharya1997},
+ PDF = {bhattacharya1997a.plastids.pdf},
+ KEYWORDS = {actin; cyanelle; endosymbiosis; Glaucocystophyta; phylogeny; small subunit ribosomal DNA}
+ }
+
+ at INCOLLECTION{bhattacharya1997b,
+ AUTHOR = {Bhattacharya, Debashish},
+ TITLE = {An Introduction to Algal Phylogeny and Phylogenetic Methods},
+ YEAR = 1997,
+ PAGES = {1-12},
+ EDITOR = {Bhattacharya, Debashish},
+ BOOKTITLE = {The Origin of Algae an their Plastids},
+ PUBLISHER = {Springer},
+ ADDRESS = {Wien},
+ CROSSREF = {bhattacharya1997},
+ KEYWORDS = {actin; cyanelle; endosymbiosis; Glaucocystophyta; phylogeny; small subunit ribosomal DNA}
+ }
+
+ at INCOLLECTION{bhattacharya1999,
+ AUTHOR = {Bhattacharya, Debashish and Friedl, Thomas and Schmidt, Heiko A.},
+ TITLE = {The Phylogeny of Thermophiles and Hyperthermophiles and the Three Domains of Life},
+ YEAR = 1999,
+ PAGES = {291-304},
+ EDITOR = {Seckbach, Joseph},
+ BOOKTITLE = {Enigmatic Microorganisms and Life in Extreme Environments},
+ PUBLISHER = {Kluwer Academic Publishers},
+ ADDRESS = {Dordrecht, Netherlands},
+ PDF = {bhattacharya1999.xphiles.pdf},
+ KEYWORDS = {}
+ }
+
+ at INPROCEEDINGS{bicego2003,
+ AUTHOR = {Bicego, Manuele and Murino, Vittorio and Figueiredo, M{\'a}rio A. T.},
+ YEAR = 2003,
+ TITLE = {Similarity-Based Clustering of Sequences Using Hidden Markov Models},
+ BOOKTITLE = {Proceedings of the 3rd International Conference on Machine Learning and Data Mining in Pattern Recognition (MLDM 2003)},
+ PAGES = {86-95},
+ SERIES = {Lecture Notes in Computer Science},
+ VOLUME = {2734},
+ MONTH = {July},
+ PUBLISHER = {Springer},
+ ADDRESS = {Heidelberg},
+ PDF = {bicego2003.lncs.pdf},
+ DOI = {},
+ PMID = {-},
+ KEYWORDS = {HMM; Hidden Markov Models; Sequence Clustering; Similarity}
+ }
+
+ at ARTICLE{bickel2000,
+ AUTHOR = {Bickel, David R.},
+ YEAR = 2000,
+ TITLE = {Implications of Fluctuations in Substitution Rates: Impact on the Uncertainty of Branch Lengths and on Relative-Rate Tests},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 50,
+ PAGES = {381-390},
+ PDF = {bickel2000.jme.pdf},
+ DOI = {10.1007/s002399910041},
+ PMID = {10795829},
+ KEYWORDS = {Branch length; Divergence time; Confidence interval; Relative rate; Molecular clock; Fractal model}
+ }
+
+ at ARTICLE{bielawski2001,
+ AUTHOR = {Bielawski, Joseph P. and Yang, Ziheng},
+ YEAR = 2001,
+ TITLE = {Positive and Negative Selection in the DAZ Gene Family},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 18,
+ PAGES = {523-529},
+ PDF = {bielawski2001.mbe.pdf},
+ DOI = {},
+ PMID = {11264403},
+ KEYWORDS = {DAZ; DAZL1; gene family; maximum likelihood; codon model; positive selection}
+ }
+
+ at ARTICLE{billera2001,
+ AUTHOR = {Billera, Louis J. and Holmes, Susan P. and Vogtmann, Karen},
+ YEAR = 2001,
+ TITLE = {Geometry of the Space of Phylogenetic Trees},
+ JOURNAL = {Adv. Appl. Math.},
+ VOLUME = 27,
+ PAGES = {733-767},
+ PDF = {billera2001.adv-appl-math.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {phylogenetic trees; semi-labeled trees; associahedron; CAT(0) space; consensus; bootstrap}
+ }
+
+ at ARTICLE{bininda1998,
+ AUTHOR = {Bininda-Emonds, Olaf R. and Bryant, Harold N.},
+ YEAR = 1998,
+ TITLE = {Properties of Matrix Representation with Parsimony Analyses},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 47,
+ PAGES = {497-508},
+ PDF = {pov1998.syst-biol-47.3.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {MRP; supertrees; Matrix Representation wit h Parsimony Analyses}
+ }
+
+ at ARTICLE{bininda1999,
+ AUTHOR = {Bininda-Emonds, O. R. and Gittleman J. L. and Purvis, A.},
+ YEAR = 1999,
+ TITLE = {Building large trees by combining phylogenetic information: A complete phylogeny of the extant {Carnivora} ({Mammalia})},
+ JOURNAL = {Biol. Rev.},
+ LONGJOURNAL = {Biol. Rev. Camb. Phil. Soc.},
+ VOLUME = 74,
+ PAGES = {143-175},
+ PDF = {bininda1999.biol-rev.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Carnivora; character congruence; taxonomic congruence; supertree; matrix representation; parsimony; divergence times; fossil dates; molecular clock; macroevolution}
+ }
+
+ at ARTICLE{bininda2001,
+ AUTHOR = {Bininda-Emonds, Olaf R. P.},
+ YEAR = 2001,
+ TITLE = {Factors Influencing Phylogenetic Inference: A Case Study Using the Mammalian Carnivores},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 16,
+ PAGES = {113-126},
+ PDF = {bininda2001.mpe.pdf},
+ DOI = {10.1006/mpev.2000.0772},
+ PMID = {10877944},
+ KEYWORDS = {Accuracy; matrix representation; missing data; MRP; phylogenetic supertrees; resolution; taxonomic congruence; total evidence}
+ }
+
+ at ARTICLE{bininda2001a,
+ AUTHOR = {Bininda-Emonds, Olaf R. P.},
+ YEAR = 2001,
+ TITLE = {Making sense of mammals},
+ JOURNAL = {TREE},
+ VOLUME = 16,
+ PAGES = {427},
+ PDF = {bininda2001a.tree.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {mammalian evolution; supertree}
+ }
+
+ at ARTICLE{bininda2001b,
+ AUTHOR = {Bininda-Emonds, Olaf R. P. and Decker-Flum, Denise M. and Gittleman, John L.},
+ YEAR = 2001,
+ TITLE = {The utility of chemical signals as phylogenetic characters: An example from the {Felidae}},
+ JOURNAL = {Biol. J. Linn. Soc.},
+ VOLUME = 72,
+ PAGES = {1-15},
+ PDF = {bininda2001b.biol-j-linn-soc.pdf},
+ DOI = {10.1006/bijl.2000.0492},
+ PMID = {},
+ KEYWORDS = {phylogeny; systematics; Felidae; chemical signals; lipids; evolution}
+ }
+
+ at ARTICLE{bininda2001c,
+ AUTHOR = {Bininda-Emonds, Olaf R. P. and Sanderson, Michael J.},
+ YEAR = 2001,
+ TITLE = {Assessment of the Accuracy of Matrix Representation with Parsimony Analysis Supertree Construction},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 50,
+ PAGES = {565-579},
+ PDF = {bininda2001c.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Accuracy; matrix representation; missing data; MRP; phylogenetic supertrees; resolution; taxonomic congruence; total evidence}
+ }
+
+ at INPROCEEDINGS{bininda2002,
+ AUTHOR = {Bininda-Emonds, Olaf R. P.},
+ YEAR = 2002,
+ TITLE = {{MRP} Supertree Construction in the Consensus Setting},
+ BOOKTITLE = {Bioconsensus: Proceedings of Tutorial and Workshop on Bioconsensus {II}},
+ SERIES = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
+ MONTH = {May},
+ ADDRESS = {},
+ PAGES = {N.N.},
+ PDF = {bininda2002.Bioconsensus2002.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Consensus; matrix representation; parsimony; supertree construction}
+ }
+
+ at ARTICLE{bininda2002a,
+ AUTHOR = {Bininda-Emonds, Olaf R. P.},
+ YEAR = 2002,
+ TITLE = {Supertrees versus Godzilla},
+ JOURNAL = {TREE},
+ VOLUME = 17,
+ PAGES = {305},
+ PDF = {bininda2002a.tree.pdf},
+ DOI = {10.1016/S0169-5347(02)02534-X},
+ PMID = {},
+ KEYWORDS = {supertrees; phylogeny; dinosaurs; paleontology; evolutionary history; phylogenetics}
+ }
+
+ at ARTICLE{bininda2002b,
+ AUTHOR = {Bininda-Emonds, Olaf R. P.},
+ YEAR = 2002,
+ TITLE = {Sealing the fate of a historical taxonomy},
+ JOURNAL = {TREE},
+ VOLUME = 17,
+ PAGES = {109},
+ PDF = {bininda2002b.tree.pdf},
+ DOI = {10.1016/S0169-5347(02)02448-5},
+ PMID = {},
+ KEYWORDS = {seals; sea lions; taxonomy; classification}
+ }
+
+ at ARTICLE{bininda2002c,
+ AUTHOR = {Bininda-Emonds, Olaf R. P. and Gittleman, John L. and Steel, Mike A.},
+ YEAR = 2002,
+ TITLE = {The (Super)Tree of Life: Procedures, Problems, and Prospects},
+ JOURNAL = {Annu. Rev. Ecol. Syst.},
+ VOLUME = 33,
+ PAGES = {265-289},
+ PDF = {bininda2002c.annu-rev-ecol-syst.pdf},
+ DOI = {10.1146/annurev.ecolsys.33.010802.150511},
+ PMID = {},
+ KEYWORDS = {matrix representation; consensus techniques; total evidence; trees; algorithms; macroevolution; biodiversity}
+ }
+
+ at ARTICLE{bininda2003,
+ AUTHOR = {Bininda-Emonds, Olaf R. P.},
+ YEAR = 2003,
+ TITLE = {Novel Versus Unsupported Clades: Assessing the Qualitative Support for Clades in {MRP} Supertrees},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 52,
+ PAGES = {839-848},
+ PDF = {bininda2003.syst-biol.pdf},
+ DOI = {10.1080/10635150390252242},
+ PMID = {},
+ KEYWORDS = {supertrees;; Carnivora; conflict; Lagomorpha; matrix representation; MRP; phylogenetic supertrees; simulation; support}
+ }
+
+ at ARTICLE{bininda2003a,
+ AUTHOR = {Bininda-Emonds, Olaf R. P.},
+ YEAR = 2003,
+ TITLE = {Supertrees Are a Necessary Not-So-Evil: A Comment on Gatesy et al.},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 52,
+ PAGES = {724-729},
+ PDF = {bininda2003a.syst-biol.pdf},
+ DOI = {10.1080/10635150390235647},
+ PMID = {},
+ KEYWORDS = {supertrees;; }
+ }
+
+ at ARTICLE{bininda2004,
+ AUTHOR = {Bininda-Emonds, Olaf R. P.},
+ YEAR = 2004,
+ TITLE = {The evolution of supertrees},
+ JOURNAL = {TREE},
+ VOLUME = 19,
+ PAGES = {in press},
+ PDF = {bininda2004.tree-manuscript.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertrees;; }
+ }
+
+ at ARTICLE{bininda2004a,
+ AUTHOR = {Bininda-Emonds, Olaf R. P.},
+ YEAR = 2004,
+ TITLE = {Trees versus characters and the supertree / supermatrix ''paradox''},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 53,
+ PAGES = {360-361},
+ PDF = {bininda2004a.syst-biol.pdf},
+ DOI = {10.1080/10635150490440396},
+ PMID = {},
+ KEYWORDS = {supertrees;; congruence; conservation; fossils; hidden support; phylogenetic hypothesis; pseudoreplication; supermatrix; supertree}
+ }
+
+ at INCOLLECTION{bininda2004b,
+ AUTHOR = {Bininda-Emonds, Olaf R. P. and Jones, Kate E. and Price, Samantha A. and Cardillo, Marcel and Grenyer, Richard and Purvis, Andy},
+ TITLE = {Garbage in, garbage out: data issues in supertree construction},
+ YEAR = 2004,
+ PAGES = {in press},
+ EDITOR = {Bininda-Emonds, Olaf R. P.},
+ BOOKTITLE = {Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life},
+ PUBLISHER = {Kluwer Academic},
+ ADDRESS = {Dordrecht, The Netherlands},
+ PDF = {bininda2004b.supertrees.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertrees;; garbage; character data; data non-independence; monophyly; paraphyly; source trees}
+ }
+
+ at INCOLLECTION{bininda2004c,
+ AUTHOR = {Bininda-Emonds, Olaf R. P.},
+ TITLE = {New uses for old phylogenies: an introduction to the volume},
+ YEAR = 2004,
+ PAGES = {in press},
+ EDITOR = {Bininda-Emonds, Olaf R. P.},
+ BOOKTITLE = {Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life},
+ PUBLISHER = {Kluwer Academic},
+ ADDRESS = {Dordrecht, The Netherlands},
+ PDF = {bininda2004c.supertrees.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertrees;; }
+ }
+
+ at ARTICLE{birney2004,
+ AUTHOR = {Birney, Ewan and Andrews, T. Daniel and Bevan, Paul and Caccamo, Mario and Chen, Yuan and Clarke, Laura and Coates, Guy and Cuff, James and Curwen, Val and Cutts, Tim and Down, Thomas and Eyras, Eduardo and Fernandez-Suarez, Xose M. and Gane, Paul and Gibbins, Brian and Gilbert, James and Hammond, Martin and Hotz, Hans-Rudolf and Iyer, Vivek and Jekosch, Kerstin and Kahari, Andreas and Kasprzyk, Arek and Keefe, Damian and Keenan, Stephen and Lehvaslaiho, Heikki and McVick [...]
+ YEAR = 2004,
+ TITLE = {An Overview of Ensembl},
+ JOURNAL = {Genome Res.},
+ VOLUME = 14,
+ PAGES = {925-928},
+ PDF = {birney2004.genome-res.pdf},
+ DOI = {10.1101/gr.1860604},
+ PMID = {15078858},
+ REMARK = {Ensembl special issue in Genome Res. 14(5)},
+ KEYWORDS = {Ensembl; EST}
+ }
+
+ at ARTICLE{birney2004,
+ AUTHOR = {Birney, Ewan and Clamp, Michele and Durbin, Richard},
+ YEAR = 2004,
+ TITLE = {{GeneWise} and {Genomewise}},
+ JOURNAL = {Genome Res.},
+ VOLUME = 14,
+ PAGES = {988-995},
+ PDF = {birney2004a.genome-res.pdf},
+ DOI = {10.1101/gr.1865504},
+ PMID = {15123596},
+ REMARK = {Ensembl special issue in Genome Res. 14(5)},
+ KEYWORDS = {Ensembl; GeneWise; gene structure prediction; Genomewise; gene structure final parse; cDNA- and EST-defined spliced structure}
+ }
+
+ at INPROCEEDINGS{birov1999,
+ AUTHOR = {Birov, Lubomir and Prokofiev, Arkady and Bartenev, Yuri and Vargin, Anatoly and Purkayastha, Avijit and Dandass, Yoginder and Erzunov, Vladimir and Shanikova, Elena and Skjellum, Anthony and Bangalore, Purushotham and Shuvalov, Eugeny and Ovechkin, Vitaly and Frolova, Nataly and Orlov, Sergey and Egorov, Sergey},
+ YEAR = 1999,
+ TITLE = {The Parallel Mathematical Libraries Project ({PMLP}): Overview, Design Innovations, and Preliminary Results},
+ BOOKTITLE = {Proceedings of the 5th International Conference on Parallel Computing Technologies (PaCT-99)},
+ SERIES = {Lecture Notes in Computer Science},
+ VOLUME = 1662,
+ PAGES = {186-193},
+ PUBLISHER = {Springer},
+ ADDRESS = {New York},
+ PDF = {birov1999.LNCS.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel computing; Parallel Mathematical Libraries Project}
+ }
+
+ at ARTICLE{bishof2000,
+ AUTHOR = {Bischof, Stefan and Ebner, Ralf and Erlebach, Thomas},
+ YEAR = 2000,
+ TITLE = {Parallel Load Balancing for Problems with Good Bisectors},
+ JOURNAL = {J. Parallel Distrib. Comput.},
+ VOLUME = 60,
+ PAGES = {1047-1073},
+ PDF = {bishof2000.jpdc.pdf},
+ DOI = {10.1006/jpdc.2000.1647},
+ PMID = {-},
+ KEYWORDS = {parallel computing; scheduling; Parallel Load Balancing}
+ }
+
+ at ARTICLE{blake2000,
+ AUTHOR = {Blake, J. A. and Eppig, J T. and Richardson, J. E. and Davidson, M. T. and {the Mouse Genome Database Group}},
+ YEAR = 2000,
+ TITLE = {The {M}ouse {G}enome {D}atabase ({MGD}): Expanding Genetic and Genomic Resources for the Laboratory Mouse},
+ JOURNAL = {Nucleic Acids Res.},
+ VOLUME = 28,
+ PAGES = {108-111},
+ PDF = {blake2000.nar.pdf},
+ DOI = {},
+ PMID = {10592195},
+ KEYWORDS = {}
+ }
+
+ at INPROCEEDINGS{blanchette1997,
+ AUTHOR = {Blanchette, M. and Bourque, G. and Sankoff, D.},
+ YEAR = 1997,
+ TITLE = {Breakpoint phylogenies},
+ BOOKTITLE = {Proceedings of the Genome Informatics Workshop VIII},
+ PAGES = {25-34},
+ MONTH = {December},
+ PUBLISHER = {Universal Academy Press},
+ PDF = {blanchette1997.GIW1997.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {breakpoint; gene order phylogeny}
+ }
+
+ at ARTICLE{blanchette1999,
+ AUTHOR = {Blanchette, Mathieu and Kunisawa, Takashi and Sankoff, David},
+ TITLE = {Gene Order Breakpoint Evidence in Animal Mitochondrial Phylogeny},
+ JOURNAL = {J. Mol. Biol.},
+ YEAR = 1999,
+ VOLUME = 49,
+ PAGES = {193-203},
+ PDF = {blanchette1999.jme.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {genomic distance; genome rearrangement; breakpoint analysis; mitochondial gene order; conserved segment; metazoan phylogeny}
+ }
+
+ at ARTICLE{blanchette2002,
+ AUTHOR = {Blanchette, Mathieu and Schwikowski, Benno and Tompa, Martin},
+ TITLE = {Algorithms for Phylogenetic Footprinting},
+ JOURNAL = {J. Comput. Biol.},
+ YEAR = 2002,
+ VOLUME = 9,
+ PAGES = {211-223},
+ PDF = {blanchette2002.jcb.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {phylogenetic footprinting; motif finding; regulatory elements; phylogeny; algorithm}
+ }
+
+ at ARTICLE{blanchette2002a,
+ AUTHOR = {Blanchette, Mathieu and Tompa, Martin},
+ TITLE = {Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting},
+ JOURNAL = {Genome Res.},
+ YEAR = 2002,
+ VOLUME = 12,
+ PAGES = {739-748},
+ PDF = {blanchette2002a.genome-res.pdf},
+ DOI = {},
+ PMID = {11997340},
+ KEYWORDS = {phylogenetic footprinting; motif finding; regulatory elements; phylogeny; algorithm}
+ }
+
+ at ARTICLE{blouin2003,
+ AUTHOR = {Blouin, Michael S.},
+ YEAR = 2003,
+ TITLE = {{DNA}-based methods for pedigree reconstruction and kinship analysis in natural populations},
+ JOURNAL = {TREE},
+ VOLUME = 18,
+ PAGES = {503-511},
+ PDF = {blouin2003.tree.pdf},
+ DOI = {10.1016/S0169-5347(03)00225-8},
+ PMID = {},
+ KEYWORDS = {pedigree reconstruction; DNA; natural populations; kinship analysis}
+ }
+
+ at TECHREPORT{blum1993,
+ AUTHOR = {Blum, Norbert},
+ YEAR = 1993,
+ MONTH = {February},
+ TITLE = {On Locally Optimal Alignments in Genetic Sequences (Revised Version)},
+ TYPE = {Research Report},
+ INSTITUTION = {Institut f{\"u}r Informatik der Universit{\"a}t Bonn},
+ NUMBER = {8567-CS},
+ ISSN = {0177-3623},
+ PDF = {hardcopy},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {}
+ }
+
+ at TECHREPORT{blum1993a,
+ AUTHOR = {Blum, Norbert},
+ YEAR = 1993,
+ MONTH = {February},
+ TITLE = {Efficient Computation of All Optimal Alignments of Two Genetic Sequences with Concave Weighting Function},
+ TYPE = {Research Report},
+ INSTITUTION = {Institut f{\"u}r Informatik der Universit{\"a}t Bonn},
+ NUMBER = {8586-CS},
+ ISSN = {0177-3623},
+ PDF = {hardcopy},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {}
+ }
+
+ at TECHREPORT{blum1993b,
+ AUTHOR = {Blum, Norbert},
+ YEAR = 1993,
+ MONTH = {February},
+ TITLE = {On Locally Optimal Local Alignments and Subalignments of Genetic Sequences with Concave Weighting Function},
+ TYPE = {Research Report},
+ INSTITUTION = {Institut f{\"u}r Informatik der Universit{\"a}t Bonn},
+ NUMBER = {8587-CS},
+ ISSN = {0177-3623},
+ PDF = {hardcopy},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {}
+ }
+
+ at TECHREPORT{blum1993c,
+ AUTHOR = {Blum, Norbert},
+ YEAR = 1993,
+ MONTH = {February},
+ TITLE = {Some Remarks on the Accurate Notation of Local Optimality in Genetic Sequences},
+ TYPE = {Research Report},
+ INSTITUTION = {Institut f{\"u}r Informatik der Universit{\"a}t Bonn},
+ NUMBER = {8588-CS},
+ NOTE = {ISSN 0177-3623},
+ PDF = {hardcopy},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {}
+ }
+
+ at INPROCEEDINGS{boc2003,
+ AUTHOR = {Boc, Alix and Makarenkov, Vladimir},
+ YEAR = 2003,
+ TITLE = {New Efficient Algorithm for Detection of Horizontal Gene Transfer Events},
+ BOOKTITLE = {Proceedings of the 3rd International Workshop on Algorithms in Bioinformatics (WABI 2003)},
+ PAGES = {190-201},
+ SERIES = {Lecture Notes in Computer Science},
+ VOLUME = {2812},
+ MONTH = {September},
+ PUBLISHER = {Springer},
+ ADDRESS = {New York},
+ PDF = {boc2003.lncs.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {lateral gene transfer; horizontal gene transfer; efficient algorithm}
+ }
+
+ at ARTICLE{bocchetta2000,
+ AUTHOR = {Bocchetta, Maurizio and Gribaldo, Simonetta and Sanangelantoni, Annamaria and Cammarano, Piero},
+ YEAR = 2000,
+ TITLE = {Phylogenetic Depth of the Bacterial Genera Aquifex and Thermotoga Inferred from Analysis of Ribosomal Protein, Elongation Factor, and {RNA} Polymerase Subunit Sequences},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 50,
+ PAGES = {366-380},
+ PDF = {bocchetta2000.jme.pdf},
+ DOI = {10.1007/s002399910040},
+ PMID = {10795828},
+ KEYWORDS = {Bacterial rooting; Hyperthermophily; Ribosomal proteins; Elongation factors; RNA polymerase; Mycoplasmatales; S10 operon; Streptomycin operon; rpoBC operon}
+ }
+
+ at INPROCEEDINGS{bodlaender1992,
+ AUTHOR = {Bodlaender, H. and Fellows, M. and Warnow, T.},
+ YEAR = 1992,
+ TITLE = {Two strikes against perfect phylogeny},
+ BOOKTITLE = {Proceedings of the 19th International Colloquium on Automata, Language, and Programming (ICALP 1992)},
+ SERIES = {Lecture Notes in Computer Science},
+ VOLUME = 623,
+ PAGES = {273-283},
+ PUBLISHER = {Springer},
+ ADDRESS = {New York},
+ PDF = {bodlaender1992.LNCS-TR.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {NP-completeness; phylogeny}
+ }
+
+ at ARTICLE{bodlaender1998,
+ AUTHOR = {Bodlaender, Hans L. and Hagerup, Torben},
+ YEAR = 1998,
+ TITLE = {Parallel Algorithms with Optimal Speedup for Bounded Treewidth},
+ JOURNAL = {SIAM J. Comput.},
+ VOLUME = 27,
+ PAGES = {1725-1746},
+ PDF = {bodlaender1998.siam-j-comput.pdf},
+ DOI = {10.1137/S0097539795289859},
+ PMID = {},
+ KEYWORDS = {parallel computing;; graph algorithms, parallel algorithms, treewidth, tree decomposition, monadic second-order logic, graph reduction, derandomization, pathwidth, partial k-trees}
+ }
+
+ at ARTICLE{bodlaender2003,
+ AUTHOR = {Bodlaender, Hans L. and Rotics, Udi},
+ YEAR = 2003,
+ TITLE = {Computing the Treewidth and the Minimum Fill-In with the Modular Decomposition},
+ JOURNAL = {Algorithmica},
+ VOLUME = 36,
+ PAGES = {375-408},
+ PDF = {bodlaender2003.algorithmica.pdf},
+ DOI = {10.1007/s00453-003-1026-5},
+ PMID = {},
+ KEYWORDS = {Treewidth; Minimum Fill-In}
+ }
+
+ at ARTICLE{boecker1999,
+ AUTHOR = {B{\"o}cker, Sebastian and Dress, Andreas W. M. and Steel, Mike A.},
+ YEAR = 1999,
+ TITLE = {Patching Up X-trees},
+ JOURNAL = {Ann. Combin.},
+ VOLUME = 3,
+ PAGES = {1-12},
+ PDF = {boecker1999.ann-comb.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {trees; supertrees; tree amalgamation; quartet encodings of trees; hierarchies; patch-works}
+ }
+
+ at PHDTHESIS{boecker1999a,
+ AUTHOR = {B{\"o}cker, Sebastian},
+ YEAR = 1999,
+ TITLE = {From Subtrees to Supertrees},
+ SCHOOL = {Fakult{\"a}t f{\"u}r Mathematik, Universit{\"a}t Bielefeld},
+ ADDRESS = {Bielefeld, Germany},
+ PDF = {boecker1999.phdthesis.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertrees;; Subtrees; Supertrees}
+ }
+
+ at ARTICLE{boecker2000,
+ AUTHOR = {B{\"o}cker, Sebastian and Bryant, David and Dress, Andreas W. M. and Steel, Mike A.},
+ YEAR = 2000,
+ TITLE = {Algorithmic Aspects of Tree Amalgamation},
+ JOURNAL = {J. Alg.},
+ VOLUME = 37,
+ PAGES = {522-537},
+ PDF = {boecker2000.j-alg.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {trees; algorithms; dyadic closure; tree amalgamation; supertrees}
+ }
+
+ at INCOLLECTION{boecker2004,
+ AUTHOR = {B{\"o}cker, Sebastian},
+ TITLE = {Unrooted Supertrees: Limitations, Traps, and Phylogenetic Patchworks},
+ YEAR = 2004,
+ PAGES = {in press},
+ EDITOR = {Bininda-Emonds, Olaf R. P.},
+ BOOKTITLE = {Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life},
+ PUBLISHER = {Kluwer Academic},
+ ADDRESS = {Dordrecht, The Netherlands},
+ PDF = {boecker2004.supertrees.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertrees;; Unrooted Supertrees; Limitations; Traps; Phylogenetic Patchworks}
+ }
+
+
+ at ARTICLE{boeckmann2003,
+ AUTHOR = {Boeckmann, Brigitte and Bairoch, Amos and Apweiler, Rolf and Blatter, Marie-Claude and Estreicher, Anne and Gasteiger, Elisabeth and Martin, Maria J. and Michoud, Karine and O'Donovan, Claire and Phan, Isabelle and Pilbout, Sandrine and Schneider, Michel},
+ YEAR = 2003,
+ TITLE = {The {SWISS-PROT} protein knowledgebase and its supplement {TrEMBL} in 2003},
+ JOURNAL = {Nucleic Acids Res.},
+ VOLUME = 31,
+ PAGES = {365-370},
+ PDF = {boeckmann2003.nar.pdf},
+ DOI = {10.1093/nar/gkg095},
+ PMID = {12520024},
+ KEYWORDS = {SwissProt; TrEMBL}
+ }
+
+ at ARTICLE{boehlke2002,
+ AUTHOR = {B\"{o}hlke, Kristina and M. Pisani, Francesca and Rossi, Mos\`{e} and Antranikian, Garabed},
+ YEAR = 2002,
+ TITLE = {Archaeal {DNA} replication: spotlight on a rapidly moving field},
+ JOURNAL = {Extremophiles},
+ VOLUME = 6,
+ PAGES = {21-31},
+ PDF = {boehlke2002.extremophiles.pdf},
+ DOI = {10.1007/s007920100222},
+ PMID = {},
+ KEYWORDS = {Euryarchaea; Crenarchaea; DNA polymerase - DNA replication - Archaeal replication fork}
+ }
+
+ at ARTICLE{boeke2003,
+ AUTHOR = {Boeke, Jef D.},
+ YEAR = 2003,
+ TITLE = {The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis},
+ JOURNAL = {Genome Res.},
+ VOLUME = 13,
+ PAGES = {1975-1983},
+ PDF = {boeke2003.genome-res.pdf},
+ DOI = {10.1101/gr.1392003},
+ PMID = {12952870},
+ KEYWORDS = {Retrotransposons; Unusual Phylogenetic Distribution}
+ }
+
+ at ARTICLE{boffelli2004,
+ AUTHOR = {Boffelli, Dario and Nobrega, Marcelo A. and Rubin Edward M.},
+ YEAR = 2004,
+ TITLE = {Comparative Genomics at the Vertebrate Extremes},
+ JOURNAL = {Nat. Rev. Genet.},
+ VOLUME = 5,
+ PAGES = {456-465},
+ PDF = {boffelli2004.nat-rev-genet.pdf},
+ DOI = {10.1038/nrg1350},
+ PMID = {},
+ KEYWORDS = {Comparative Genomics; Vertebrates}
+ }
+
+ at ARTICLE{boldogkoi2000,
+ AUTHOR = {Boldogk{\"o}i, Zsolt},
+ YEAR = 2000,
+ TITLE = {Coding in the Noncoding {DNA} Strand: A Novel Mechanism of Gene Evolution?},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 51,
+ PAGES = {600-606},
+ PDF = {boldogkoi2000.jme.pdf},
+ DOI = {10.1007/s002390010123},
+ PMID = {11116333},
+ KEYWORDS = {Antisense DNA strand; Overlapping ORF; Gene evolution; Genetic Code; Codon usage; G+C content}
+ }
+
+ at ARTICLE{bollback2001,
+ AUTHOR = {Bollback, Jonathan P. and Huelsenbeck, John P.},
+ YEAR = 2001,
+ TITLE = {Phylogeny, Genome Evolution, and Host Specificity of Single-Stranded {RNA} Bacteriophage (Family {Leviviridae})},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 52,
+ PAGES = {117-128},
+ PDF = {bollback2001.jme.pdf},
+ DOI = {10.1007/s002390010140},
+ PMID = {11231891},
+ KEYWORDS = {Phylogeny; Genome evolution; Levi-viridae; RNA bacteriophage; Replicase gene; Coat gene; Bayesian inference; Markov chain Monte Carlo}
+ }
+
+ at ARTICLE{bollback2002,
+ AUTHOR = {Bollback, Jonathan P.},
+ YEAR = 2002,
+ TITLE = {Bayesian Model Adequacy and Choice in Phylogenetics},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 19,
+ PAGES = {1171-1180},
+ PDF = {bollback2002.mbe.pdf},
+ DOI = {},
+ PMID = {12082136},
+ KEYWORDS = {phylogenetics; Bayesian inference; model determination; model selection; model adequacy; posterior predictive densities; posterior predictive simulations}
+ }
+
+ at ARTICLE{bollyky1999,
+ AUTHOR = {Bollyky, Paul L. and Holmes, Edward C.},
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+ YEAR = 1999,
+ VOLUME = 49,
+ PAGES = {130-141},
+ PDF = {bollyky1999.jme.pdf},
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+ PMID = {},
+ KEYWORDS = {Hepatitis B virus; phylogeny; genotypes; gamma distribution; molecular clock}
+ }
+
+ at ARTICLE{bolshoy1996,
+ AUTHOR = {Bolshoy, Alexander and Ioshikhes, Ilya and Trifonov, Edward N.},
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+ AUTHOR = {Bolten, Eva and Schliep, Alexander and Schneckener, Sebastian and Schomburg, Dietmar and Schrader, Rainer},
+ YEAR = 2001,
+ TITLE = {Clustering protein sequences -- structure prediction by transitive homology},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 17,
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+ DOI = {},
+ PMID = {11673238},
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+ at BOOK{bourrelly1970,
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+
+ at ARTICLE{bohnert1982,
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+ YEAR = 2002,
+ TITLE = {Genetic Algorithms and Parallel Processing in Maximum-Likelihood Phylogeny Inference},
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+ KEYWORDS = {parallel bioinformatics; parallel computing; genetic algorithm; phylogeny inference; maximum likelihood; parallel algorithm; nucleotide sequence data}
+ }
+
+ at ARTICLE{braun2002,
+ AUTHOR = {Braun, Edward L. and Kimball, Rebecca T.},
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+ PAGES = {614-625},
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+ KEYWORDS = {Mitochondrial Sequences; Model Complexity; Taxon Sampling; Sequence Length}
+ }
+
+ at ARTICLE{brehm2003,
+ AUTHOR = {Brehm, A. and Jesus, J. and Sp\'{i}nola, H. and Alves, C. and Vicente, L. and Harris, D. J.},
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+ TITLE = {Phylogeography of the {Madeiran} endemic lizard {Lacerta dugesii} inferred from {mtDNA} sequences},
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+ PAGES = {222-230},
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+ DOI = {10.1016/S1055-7903(02)00310-X},
+ PMID = {},
+ KEYWORDS = {Lacerta dugesii; 12S rRNA; Cytochrome b; Phylogeography; Madeira}
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+ at ARTICLE{breiman2001,
+ AUTHOR = {Breiman, Leo},
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+ AUTHOR = {Brinkman, Fiona S.L. and Blanchard, Jeffrey L. and Cherkasov, Artem and Av-Gay, Yossef and Brunham, Robert C. and Fernandez, Rachel C. and Finlay, B. Brett and Otto, Sarah P. and Ouellette, B. F. Francis and Keeling, Patrick J. and Rose, Ann M. and Hancock, Robert E.W. and Greberg, Hans and Jones, Steven J.M.},
+ YEAR = 2002,
+ TITLE = {Evidence That Plant-Like Genes in {Chlamydia} Species Reflect an Ancestral Relationship between {Chlamydiaceae}, {Cyanobacteria}, and the {Chloroplast}},
+ JOURNAL = {Genome Res.},
+ VOLUME = 12,
+ PAGES = {1159-1167},
+ PDF = {brinkman2002.genome-res.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{brinkmann1999,
+ AUTHOR = {Brinkmann, Henner and Philippe, Herv\'{e}},
+ YEAR = 1999,
+ TITLE = {Archaea Sister Group of Bacteria? Indications from Tree Reconstruction Artifacts in Ancient Phylogenies},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 16,
+ PAGES = {817-825},
+ PDF = {brinkmann1999.mbe.pdf},
+ DOI = {},
+ PMID = {10368959},
+ KEYWORDS = {Archea; Bacteria; eukaryotes; molecular phylogeny; long-branch attraction artifact; signal recognition particle}
+ }
+
+ at ARTICLE{britton2002,
+ AUTHOR = {Britton, Tom and Oxelman, Bengt and Vinnersten, Annika and Bremer, K{\aa}re},
+ YEAR = 2002,
+ TITLE = {Phylogenetic dating with confidence intervals using mean path lengths},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 24,
+ PAGES = {58-65},
+ PDF = {britton2002.mpe.pdf},
+ DOI = {10.1016/S1055-7903(02)00268-3},
+ PMID = {},
+ KEYWORDS = {Confidence interval; Liliales; Molecular clock; Phylogenetic dating; Phylogenetic tree; Poisson process; Reference fossil}
+ }
+
+ at ARTICLE{brocchieri2001,
+ AUTHOR = {Brocchieri, Luciano},
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+ PAGES = {27-40},
+ PDF = {brocchieri2001.tpb.pdf},
+ DOI = {10.1006/tpbi.2000},
+ PMID = {},
+ KEYWORDS = {Phylogenetic Inferences; Molecular Sequences; Review}
+ }
+
+ at INPROCEEDINGS{brodal2001,
+ AUTHOR = {Brodal, St{\o}lting and Fagerberg, Rolf and Pedersen, Christian N. S.},
+ YEAR = 2001,
+ TITLE = {Computing the Quartet Distance Between Evolutionary Trees in Time {$O(n log^2 n)$}},
+ BOOKTITLE = {Proceedings of the 12th International Symposium on Algorithms and Computation (ISAAC 2001)},
+ MONTH = {December},
+ ADDRESS = {Christchurch, New Zealand},
+ PDF = {brodal2001.ISAAC2001.ps},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at TECHREPORT{brodal2001a,
+ AUTHOR = {Brodal, St{\o}lting and Fagerberg, Rolf and Pedersen, Christian N. S.},
+ YEAR = 2001,
+ TITLE = {Computing the Quartet Distance Between Evolutionary Trees in Time {$O(n log^2 n)$}},
+ MONTH = {May},
+ TYPE = {Alcom-FT Technical Report Series},
+ INSTITUTION = {Alcom-FT},
+ NUMBER = {ALCOMFT-TR-01-131},
+ PDF = {brodal2001a.TR.ps},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{bromham1996,
+ AUTHOR = {Bromham, Lindell and Rambaut, Andrew and Harvey, Paul H.},
+ YEAR = 1996,
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+ PDF = {bromham1996.jme.pdf},
+ DOI = {},
+ PMID = {8995058},
+ KEYWORDS = {molecular evolution; molecular clock; phylogeny; metabolic rate; generation time; body size; allometry}
+ }
+
+ at ARTICLE{bromham2000,
+ AUTHOR = {Bromham, Lindell and Penny, David and Rambaut, Andrew and Hendy, Michael D.},
+ YEAR = 2000,
+ TITLE = {The Power of Relative Rates Tests Depends on the Data},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 50,
+ PAGES = {296-301},
+ PDF = {bromham2000.jme.pdf},
+ DOI = {10.1007/s002399910034},
+ PMID = {10754073},
+ KEYWORDS = {Molecular clock; Substitution rate; Phylogeny; Molecular date estimates; Tajima test; Rate variation}
+ }
+
+ at ARTICLE{bromham2002,
+ AUTHOR = {Bromham, Lindell},
+ YEAR = 2002,
+ TITLE = {The human zoo: Endogenous retroviruses in the human genome},
+ JOURNAL = {TREE},
+ VOLUME = 17,
+ PAGES = {91-97},
+ PDF = {bromham2002.tree.pdf},
+ DOI = {10.1016/S0169-5347(01)02394-1},
+ PMID = {},
+ KEYWORDS = {transposable element; HERV; genome evolution; xenotransplantation; noncoding DNA; retrovirus; human genome project}
+ }
+
+ at ARTICLE{bromham2002a,
+ AUTHOR = {Bromham, Lindell},
+ YEAR = 2002,
+ TITLE = {Molecular Clocks in Reptiles: Life History Influences Rate of Molecular Evolution},
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+ VOLUME = 19,
+ PAGES = {302-309},
+ PDF = {bromham2002a.mbe.pdf},
+ DOI = {},
+ PMID = {11861889},
+ KEYWORDS = {molecular clock, molecular evolution, generation time effect, substitution rate, relative rates, comparative method}
+ }
+
+ at ARTICLE{bromham2003,
+ AUTHOR = {Bromham, Lindell and Eyre-Walker, Adam and Smith, Noel H. and Maynard Smith, John},
+ YEAR = 2003,
+ TITLE = {Mitochondrial {Steve}: paternal inheritance of mitochondria in humans},
+ JOURNAL = {TREE},
+ VOLUME = 18,
+ PAGES = {2-4},
+ PDF = {bromham2003.tree.pdf},
+ DOI = {10.1016/S0169-5347(02)00009-5},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{brookfield1994,
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+ at ARTICLE{brooks2002,
+ AUTHOR = {Brooks, Dawn J. and Fresco, Jacques R. and Lesk, Arthur M. and Singh, Mona},
+ YEAR = 2002,
+ TITLE = {Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 19,
+ PAGES = {1645-1655},
+ PDF = {brooks2002.mbe.pdf},
+ DOI = {},
+ PMID = {12270892},
+ KEYWORDS = {MP, maximum parsimony; ML, maximum likelihood; LUA, Last Universal Ancestor; COG, Clusters of Orthologous Groups}
+ }
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+ }
+
+ at ARTICLE{broughton2001,
+ AUTHOR = {Broughton, Richard E. and Milam, Jami E. and Roe, Bruce A.},
+ YEAR = 2001,
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+ PDF = {broughton2001.genome-res.pdf},
+ DOI = {},
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+ }
+
+ at ARTICLE{brower1996,
+ AUTHOR = {Brower, A. V. Z. and },
+ YEAR = 1996,
+ TITLE = {Gene Trees, Species Trees, and Systematics: A Cladistic Perspective},
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+ PDF = {brower1996.annu-rev-ecol-syst.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {mtDNA; phylogeny; coalescence; cladistics; empirism}
+ }
+
+ at ARTICLE{brower1999,
+ AUTHOR = {Brower, Andrew V. Z.},
+ YEAR = 1999,
+ TITLE = {Delimitation of Phylogenetic Species with {DNA} Sequences: A Critique of {Davis} and {Nixon's} Population Aggregation Analysis},
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+ VOLUME = 48,
+ PAGES = {199-213},
+ PDF = {brower1999.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Davis and Nixon's Population Aggregation Analysis}
+ }
+
+ at ARTICLE{brown1994,
+ AUTHOR = {Brown, James K.},
+ YEAR = 1994,
+ TITLE = {Bootstrap Hypothesis Tests for evolutionary Trees and other Dendrograms},
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+ VOLUME = 91,
+ PAGES = {12293-12297},
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+ KEYWORDS = {phylogeny; population structure; plant evolution; 5S rRNA; eyespot}
+ }
+
+ at ARTICLE{brown2001,
+ AUTHOR = {Brown, James K.},
+ YEAR = 2001,
+ TITLE = {Genomic and Phylogenetic Perspectives on the Evolution of Prokaryotes},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 50,
+ PAGES = {497-512},
+ PDF = {brown2001.syst-biol.pdf},
+ KEYWORDS = {Archaea; comparative genomics; eubacteria; phenylalanyl-tRNAsynthetase; universal tree}
+ }
+
+ at ARTICLE{brown2001a,
+ AUTHOR = {Brown, Celeste J. and Garner, Ethan C. and Dunker, A. Keith and Joyce, Paul},
+ YEAR = 2001,
+ TITLE = {The Power to Detect Recombination Using the Coalescent},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 18,
+ PAGES = {1421-1424},
+ PDF = {brown2001.mbe.pdf},
+ DOI = {},
+ PMID = {11420381},
+ KEYWORDS = {recombination; statistical power; gene conversion; hypothesis testing; likelihood ratio}
+ }
+
+ at ARTICLE{brown2002,
+ AUTHOR = {Brown, Eric W. and Kotewicz, Michael L. and Cebula, Thomas A.},
+ YEAR = 2002,
+ TITLE = {Detection of recombination among Salmonella enterica strains using the incongruence length difference test},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 24,
+ PAGES = {102-120},
+ PDF = {brown2002.mpe.pdf},
+ DOI = {10.1016/S1055-7903(02)00222-1},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{brown2002a,
+ AUTHOR = {Brown, Celeste J. and Takayama, Sachiko and Campen, Andrew M. and Vise, Pam and Marshall, Thomas W. and Oldfield, Christopher J. and Williams, Christopher J. and Dunker, A. Keith},
+ YEAR = 2002,
+ TITLE = {Evolutionary Rate Heterogeneity in Proteins with Long Disordered Regions},
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+ PAGES = {104-110},
+ PDF = {brown2002a.jme.pdf},
+ DOI = {10.1007/s00239-001-2309-6},
+ PMID = {},
+ KEYWORDS = {Disordered protein, Protein evolution, Rate heterogeneity}
+ }
+
+ at ARTICLE{brown2003,
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+ YEAR = 2003,
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+ DOI = {10.1038/nrg1000},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{bruck1997,
+ AUTHOR = {Bruck, Jehoshua and Dolev, Danny and Ho, Ching-Tien and Rosu, Marcel-Catalin and Strong, Ray},
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+ PAGES = {19-34},
+ PDF = {bruck1997.jpdc.pdf},
+ DOI = {10.1006/jpdc.1996.1267},
+ PMID = {-},
+ KEYWORDS = {parallel computing; message passing interface; clusters of workstations}
+ }
+
+ at ARTICLE{brudno2003,
+ AUTHOR = {Brudno, Michael and Do, Chuong B. and Cooper, Gregory M. and Kim, Michael F. and Davydov, Eugene and {NISC Comparative Sequencing Program} and Green, Eric D. and Sidow, Arend and Batzoglou, Serafim},
+ YEAR = 2003,
+ TITLE = {{LAGAN} and Multi-{LAGAN}: Efficient Tools for Large-Scale Multiple Alignment of Genomic {DNA}},
+ JOURNAL = {Genome Res.},
+ VOLUME = 13,
+ PAGES = {721-731},
+ PDF = {brudno2003.genome-res.pdf},
+ DOI = {10.1101/gr.926603},
+ PMID = {12654723},
+ KEYWORDS = {Large-Scale Multiple Alignment; Genomic DNA}
+ }
+
+ at ARTICLE{brugna2003a,
+ AUTHOR = {Brudno, Michael and Malde, Sanket and Poliakov, Alexander and Do, Chuong B. and Couronne, Olivier and Dubchak, Inna and Batzoglou, Serafim},
+ YEAR = 2003,
+ TITLE = {Glocal alignment: finding rearrangements during alignment},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 19,
+ PAGES = {i54-i62},
+ PDF = {brudno2003a.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg1005},
+ PMID = {12855437},
+ KEYWORDS = {Glocal alignment; rearrangements}
+ }
+
+ at ARTICLE{brugna2003,
+ AUTHOR = {Brugna-Guiral, Marianne and Tron, Pascale and Nitschke, Wolfgang and Stetter, Karl-Otto and Burlat, Benedicte and Guigliarelli, Bruno and Bruschi, Mireille and Giudici-Orticoni, Marie Th\'{e}r\`{e}se},
+ YEAR = 2003,
+ TITLE = {{[NiFe]} hydrogenases from the hyperthermophilic bacterium Aquifex aeolicus: properties, function, and phylogenetics},
+ JOURNAL = {Extremophiles},
+ VOLUME = 7,
+ PAGES = {145-157},
+ PDF = {brugna2003.extremophiles.pdf},
+ DOI = {10.1007/s00792-002-0306-3},
+ PMID = {},
+ KEYWORDS = {Aquifex aeolicus; Hydrogenase; Phylogeny; Hydrogen metabolism}
+ }
+
+ at ARTICLE{brumfield2003,
+ AUTHOR = {Brumfield, Robb T. and Beerli, Peter and Nickerson, Deborah A. and Edwards, Scott V.},
+ YEAR = 2003,
+ TITLE = {The utility of single nucleotide polymorphisms in inferences of population history},
+ JOURNAL = {TREE},
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+ PAGES = {249-256},
+ PDF = {brumfield2003.tree.pdf},
+ DOI = {10.1016/S0169-5347(03)00018-1},
+ PMID = {},
+ KEYWORDS = {single nucleotide polymorphisms; SNP; population history}
+ }
+
+ at ARTICLE{bry2003,
+ AUTHOR = {Fran\c{c}ois Bry and Peer Kr{\"o}ger},
+ YEAR = 2003,
+ TITLE = {A Computational Biology Database Digest: Data, Data Analysis, and Data Management},
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+ PAGES = {7-42},
+ PDF = {bry2003.dpdb.pdf},
+ DOI = {10.1023/A:1021540705916},
+ PMID = {},
+ KEYWORDS = {parallel computing; parallel bioinformatics; parallel databases;; computational biology; molecular biology databases; data analysis; data modelling; data integration}
+ }
+
+ at ARTICLE{bryant1995,
+ AUTHOR = {Bryant, David and Steel, Mike},
+ YEAR = 1995,
+ TITLE = {Extension Operations on Sets of Leaf-Labeled Trees},
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+ PAGES = {425-453},
+ PDF = {bryant1995.adv-appl-math.pdf},
+ DOI = {10.1006/aama.1995.1020},
+ PMID = {},
+ KEYWORDS = {OneTree; Supertree}
+ }
+
+ at PHDTHESIS{bryant1997,
+ AUTHOR = {Bryant, David},
+ YEAR = 1997,
+ TITLE = {Hunting for trees, building trees and comparing trees: Theory and method in phylogenetic analysis},
+ SCHOOL = {Dept. Mathematics, University of Canterbury},
+ ADDRESS = {Canterbury},
+ PDF = {bryant1997.thesisA4.ps},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{bryant1998,
+ AUTHOR = {Bryant, David and Waddell, Peter},
+ YEAR = 1998,
+ TITLE = {Rapid Evaluation of Least-Squares and Minimum-Evolution Criteria on Phylogenetic Trees},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 15,
+ PAGES = {1346-1359},
+ PDF = {bryant1998.mbe.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {least-square method; minimum evolution; phylogetic inference; tree statistics; algorithms}
+ }
+
+ at INPROCEEDINGS{bryant1999,
+ AUTHOR = {Bryant, David and Steel, Mike},
+ YEAR = 1999,
+ TITLE = {Fast Algorithms for Constructing Optimal Trees from Quartets},
+ PAGES = {147-155},
+ BOOKTITLE = {Proceedings of the ACM-SIAM Symposium on Discrete Algorithms - SODA '99},
+ MONTH = {January},
+ ADDRESS = {Baltimore, Maryland},
+ PDF = {bryant1999.SODA.pdf},
+ DOI = {10.1145/314500.314547},
+ PMID = {},
+ KEYWORDS = {optimal quartet trees; poloynomial complexity; fast algorithms; ; optimal weight binary tree}
+ }
+
+ at INPROCEEDINGS{bryant2000,
+ AUTHOR = {Bryant, David and Tsang, John and Kearney, Paul and Li, Ming},
+ YEAR = 2000,
+ TITLE = {Computing the Quartet Distance Between Evolutionary Trees},
+ BOOKTITLE = {Proceedings of the ACM-SIAM Symposium on Discrete Algorithms - SODA 2000},
+ MONTH = {January},
+ ADDRESS = {San Francisco, California},
+ PDF = {bryant2000.SODA2000.ps},
+ DOI = {10.1145/338219.338264},
+ PMID = {},
+ KEYWORDS = {Quartet distance between trees}
+ }
+
+ at ARTICLE{bryant2001,
+ AUTHOR = {Bryant, David and Steel, Mike},
+ YEAR = 2001,
+ TITLE = {Constructing optimal trees from quartets},
+ JOURNAL = {J. Alg.},
+ VOLUME = 38,
+ PAGES = {237-259},
+ PDF = {bryant2001.j-alg.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {quartets, phylogenetic trees, algorithms, consensus, networks}
+ }
+
+ at INPROCEEDINGS{bryant2001a,
+ AUTHOR = {Bryant, David},
+ YEAR = 2001,
+ TITLE = {A classification of consensus methods for phylogenetics},
+ BOOKTITLE = {Bioconsensus: Proceedings of Tutorial and Workshop on Bioconsensus {II}},
+ SERIES = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
+ PAGES = {to appear},
+ PUBLISHER = {DIMACS-AMS},
+ PDF = {bryant2001a.Bioconsensus2001.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Consensus Methods; Phylogenetics}
+ }
+
+ at ARTICLE{bryant2004,
+ AUTHOR = {Bryant, David and Moulton, Vincent},
+ YEAR = 2004,
+ TITLE = {Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 21,
+ PAGES = {255-265},
+ PDF = {bryant2004.mbe.pdf},
+ DOI = {10.1093/molbev/msh018},
+ PMID = {14660700},
+ KEYWORDS = {networks; Neighbor-Joining; recombination; SplitsTree}
+ }
+
+ at INCOLLECTION{bryant2004a,
+ AUTHOR = {Bryant, David and Semple, Charles and Steel, Mike},
+ TITLE = {Supertree methods for ancestral dates and other applications},
+ YEAR = 2004,
+ PAGES = {in press},
+ EDITOR = {Bininda-Emonds, Olaf R. P.},
+ BOOKTITLE = {Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life},
+ PUBLISHER = {Kluwer Academic},
+ ADDRESS = {Dordrecht, The Netherlands},
+ PDF = {bryant2004a.supertrees.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertrees;; BUILD; divergence dates; rooted phylogenetic tree; supertree}
+ }
+
+
+ at ARTICLE{buckley2001,
+ AUTHOR = {Buckley, Thomas R. and Simon, Chris and Chambers, Geoffrey K.},
+ YEAR = 2001,
+ TITLE = {Exploring Among-Site Rate Variation Models in a Maximum Likelihood Framework Using Empirical Data: Effects of Model Assumptions on Estimates of Topology, Branch Lengths, and Bootstrap Support},
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+ PAGES = {67-86},
+ PDF = {buckley2001.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Among-site rate variation; bootstrapping; insect mitochondrial DNA; likelihood ratio test; Maoricicada; maximum likelihood; nucleotide substitution models}
+ }
+
+ at ARTICLE{buckley2002,
+ AUTHOR = {Buckley, Thomas R. and Cunningham, Clifford W.},
+ YEAR = 2002,
+ TITLE = {The Effects of Nucleotide Substitution Model Assumptions on Estimates of Nonparametric Bootstrap Support},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 19,
+ PAGES = {394-405},
+ PDF = {buckley2002.mbe.pdf},
+ DOI = {},
+ PMID = {11919280},
+ KEYWORDS = {maximum likelihood; phylogenetics; nucleotide substitution models; nonparametric bootstrapping; model selection; AIC}
+ }
+
+ at ARTICLE{buckley2002a,
+ AUTHOR = {Buckley, Thomas R. and Arensburger, Peter and Simon, Chris and Chambers, Geoffrey K.},
+ YEAR = 2002,
+ TITLE = {Combined Data, {Bayesian} Phylogenetics, and the Origin of the {New Zealand} {Cicada} Genera},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 51,
+ PAGES = {4-18},
+ PDF = {buckley2002a.syst-biol.pdf},
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+ KEYWORDS = {AIC; Bayesian statistics; cicadas; maximum likelihood; model selection; model selection uncertainty; phylogenetics}
+ }
+
+ at ARTICLE{buckley2002b,
+ AUTHOR = {Buckley, Thomas R.},
+ YEAR = 2002,
+ TITLE = {Model Misspecification and Probabilistic Tests of Topology: Evidence from Empirical Data Sets},
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+ VOLUME = 51,
+ PAGES = {509-523},
+ PDF = {buckley2002b.syst-biol.pdf},
+ DOI = {10.1080/10635150290069922},
+ PMID = {Bayesian statistics; Markov chain Monte Carlo; maximum likelihood; nucleotide substitution models; parametric bootstrapping; SH test; SOWH test; statistical tests},
+ KEYWORDS = {Bayesian statistics; Markov chain Monte Carlo; maximum likelihood; nucleotide substitution models; parametric bootstrapping; SH test; SOWH test; statistical tests}
+ }
+
+ at ARTICLE{bull1993,
+ AUTHOR = {Bull, J. J. and Huelsenbeck, John P. and Cunningham, Clifford W. and Swofford, David L. and Waddell, Peter J.},
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+ }
+
+ at ARTICLE{bull2001,
+ AUTHOR = {Bull, J. J. and Wichman, H. A.},
+ YEAR = 2001,
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+ at BOOK{burkhardt1993,
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+ TITLE = {{Parallele} {Rechnersysteme}: {Programmierung} und {Anwendung}},
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+ PAGES = {66-82},
+ PDF = {buschbom2004.mpe.pdf},
+ DOI = {10.1016/j.ympev.2003.11.012},
+ PMID = {},
+ KEYWORDS = {Ascomycota; Homoplasy; Lecanorales; Molecular phylogenetics; Porpidia; Resolution; Taxon sampling}
+ }
+
+ at ARTICLE{bush1999,
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+ YEAR = 1999,
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+ PDF = {bush1999.science.pdf},
+ DOI = {},
+ PMID = {10583948},
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+ }
+
+ at ARTICLE{bush2000,
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+ YEAR = 2000,
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+ }
+
+ at ARTICLE{butler1997,
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+ PDF = {butler1997.evol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Ancestral Reconstruction, Brownian Motion, Gradual Evolution, Phylogenetic Comparative Method, Simulation, Speciational Evolution, Statistical Tests}
+ }
+
+
+ at ARTICLE{cabillic1997,
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+ PMID = {-},
+ KEYWORDS = {parallel computing; Networks of Heterogeneous Workstations}
+ }
+
+ at ARTICLE{caetano2002,
+ AUTHOR = {Caetano-Anoll\'{e}s, Gustavo},
+ YEAR = 2002,
+ TITLE = {Evolved {RNA} Secondary Structure and the Rooting of the Universal Tree of Life},
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+ PDF = {caetano2002.jme.pdf},
+ DOI = {10.1007/s00239-001-0048-3},
+ PMID = {11847559},
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+ }
+
+ at INPROCEEDINGS{camona1989,
+ AUTHOR = {Carmona, E. A.},
+ YEAR = 1989,
+ TITLE = {Parallelizing a large scientific code -- methods, issues, and concerns},
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+ ADDRESS = {New York, USA},
+ PDF = {camona1989.SC.pdf},
+ DOI = {10.1145/76263.76266},
+ PMID = {},
+ KEYWORDS = {parallel computing; scientific computing; scientific programming; methods; issues; concerns}
+ }
+
+ at ARTICLE{campbell2003,
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+
+ at ARTICLE{cammarano1999,
+ AUTHOR = {Cammarano, Piero and Creti, Roberta and Sanangelantoni, Anna M. and Palm, Peter},
+ YEAR = 1999,
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+ DOI = {},
+ PMID = {10486009},
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+ }
+
+ at ARTICLE{campbell2002,
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+
+ at ARTICLE{canapa1996,
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+ DOI = {},
+ PMID = {8875864},
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+
+ at ARTICLE{canback2002,
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+ }
+
+ at ARTICLE{cao1994,
+ AUTHOR = {Cao, Ying and Adachi, Jun and Yano, Take-aki and Hasegawa, Masami},
+ YEAR = 1994,
+ TITLE = {Phylogenetic place of guinea pigs: No support of the rodent-polyphyly hypothesis from maximum-likelihood analyses of multiple protein sequences},
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+ PDF = {cao1994.mbe.pdf},
+ DOI = {},
+ PMID = {8078399},
+ KEYWORDS = {Guinea pig; Caviomorpha; rodents; mammalian evolution; maximum-likelihood tree of proteins}
+ }
+
+ at ARTICLE{cao1998,
+ AUTHOR = {Cao, Ying and Adachi, Jun and Hasegawa, Masami},
+ YEAR = 1998,
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+ DOI = {},
+ PMID = {},
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+ }
+
+ at ARTICLE{cao2000,
+ AUTHOR = {Cao, Ying and Fujiwara, Miyako and Nikaido, Masato and Okada, Norihiro and Hasegawa, Masami},
+ YEAR = 2000,
+ TITLE = {Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data},
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+ KEYWORDS = {Chiroptera/Eulipotyphla clade; Maximum likelihood; Molecular phylogeny; Multiple references; Relaxed molecular clock}
+ }
+
+ at ARTICLE{cao2000a,
+ AUTHOR = {Cao, Ying and Sorenson, Michael D. and Kumazawa, Yoshinori and Mindell, David P. and Hasegawa, Masami},
+ YEAR = 2000,
+ TITLE = {Phylogenetic position of turtles among amniotes: Evidence from mitochondrial and nuclear genes},
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+ }
+
+ at ARTICLE{cao2004,
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+
+ at INPROCEEDINGS{cappello1999,
+ AUTHOR = {Cappello, Franck and Richard, Olivier and Etiemble, Daniel},
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+ PUBLISHER = {Springer},
+ ADDRESS = {New York},
+ PDF = {cappello1999.LNCS.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel computing; NAS Benchmark; Cluster of SMP PCs; Parallelization of the MPI Programs with OpenMP}
+ }
+
+ at ARTICLE{carels1998,
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+
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+ at ARTICLE{cavalli1967a,
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+ KEYWORDS = {parallel computing; teaching parallel processing, foundations of parallel programming languages, message passing interface (MPI) and bulk synchronous parallel (BSP) models}
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+ at ARTICLE{ceron1998,
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+ KEYWORDS = {parallel bioinformatics; parallel computing; hitch-hiking; maximum parsimony; parallel heuristic search}
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+ SERIES = {Preprints Mathematik},
+ NUMBER = {2002-14},
+ PUBLISHER = {Institute of Mathematics and Computer Science, Ernst--Moritz--Arndt--University},
+ ADDRESS = {Greifswald, Germany},
+ PDF = {books/cieslik2002.shortest_connectivity-2002_14.book.ps.gz},
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+ TYPE = {Tech. Rep.},
+ NUMBER = {TR02-01},
+ PDF = {chen2001.TR02-01.pdf},
+ KEYWORDS = {Supertrees; MPF; Flipping; evolutionary tree; phylogenetic tree, supertree, tree assembly; tree distance}
+ }
+
+ at INPROCEEDINGS{chen2002,
+ AUTHOR = {Chen, D. and Eulenstein, O. and Fern\'{a}ndez-Baca, D. and Sanderson, M. J.},
+ YEAR = 2002,
+ TITLE = {Supertrees by Flipping},
+ BOOKTITLE = {Proceedings of the Computing and Combinatorics Conference (COCOON 2002)},
+ SERIES = {Lecture Notes in Computer Science},
+ VOLUME = 2387,
+ PAGES = {391-400},
+ MONTH = {August},
+ PUBLISHER = {Springer},
+ ADDRESS = {Heidelberg},
+ PDF = {chen2002.LNCS.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Supertrees; MPF; Flipping; evolutionary tree; phylogenetic tree, supertree, tree assembly; tree distance}
+ }
+
+ at ARTICLE{chen2003,
+ AUTHOR = {Chen, D. and Diao, L. and Eulenstein, O. and Fern\'{a}ndez-Baca, D. and Sanderson, M. J.},
+ YEAR = 2003,
+ TITLE = {Flipping: A Supertree Construction Method},
+ JOURNAL = {DIMACS Series in Discrete Mathematics and Theoretical Computer Sciences},
+ VOLUME = 000,
+ PAGES = {to appear},
+ PDF = {chen2003.DIMACS-manuscript.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertrees; MRF; Flipping; Matrix Representation; evolutionary tree; phylogenetic tree, supertree, tree assembly; tree distance}
+ }
+
+ at ARTICLE{chen2003a,
+ AUTHOR = {Chen, Wei-Jen and Bonillo, C\'{e}line and Lecointre, Guillaume},
+ YEAR = 2003,
+ TITLE = {Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of {Acanthomorpha} ({Teleostei}) with larger number of taxa},
+ JOURNAL = {Mol. Phylogenet. Evol.},
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+ PAGES = {262-288},
+ PDF = {chen2003a.mpe.pdf},
+ DOI = {10.1016/S1055-7903(02)00371-8},
+ PMID = {},
+ KEYWORDS = {12s mtDNA; 16s mtDNA; 28s rDNA; Acanthomorpha; Teleostean phylogeny; Rhodopsin; Separate analyses; Reliability; Robustness; Taxonomic congruence; Teleostei}
+ }
+
+ at ARTICLE{chen2003b,
+ AUTHOR = {Chen, Zizhong and Dongarra, Jack and Luszczek, Piotr and Roche, Kenneth},
+ YEAR = 2003,
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+ PMID = {},
+ KEYWORDS = {parallel computing;; High performance computing; LAPACK; Linear algebra; PBLAS; ScaLAPACK; Numerical parallel libraries; Self-adapting software}
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+
+ at ARTICLE{chen2003c,
+ AUTHOR = {Chen, Zhuoran},
+ YEAR = 2003,
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+ VOLUME = 19,
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+ DOI = {},
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+ at INCOLLECTION{cotton2004,
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+
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+ PAGES = {830-840},
+ PDF = {dacks2002.mbe.pdf},
+ DOI = {},
+ PMID = {12032239},
+ KEYWORDS = {evolution; Naegleria; Cercomonas; Ochromonas; intron; nucleomorph}
+ }
+
+ at ARTICLE{dagan2002,
+ AUTHOR = {Dagan, Tal and Talmor, Yael and Graur, Dan},
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+ TITLE = {Ratios of Radical to Conservative Amino Acid Replacement are Affected by Mutational and Compositional Factors and May Not Be Indicative of Positive {Darwinian} Selection},
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+ VOLUME = 19,
+ PAGES = {1022-1025},
+ PDF = {dagan2002.mbe.pdf},
+ DOI = {},
+ PMID = {12082122},
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+ }
+
+ at INCOLLECTION{daniel2004,
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+ DOI = {},
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+
+
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+ DOI = {},
+ PMID = {},
+ KEYWORDS = {prokaryotes; phylogeny; supertree; complete genomes; horizontal gene transfers}
+ }
+
+ at ARTICLE{daubin2002,
+ AUTHOR = {Daubin, Vincent and Gouy, Manolo and Perri{\`e}re, Guy},
+ YEAR = 2002,
+ TITLE = {A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History},
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+ }
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+ YEAR = 2004,
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+ PAGES = {86-89},
+ PDF = {daubin2004.mbe.pdf},
+ DOI = {10.1093/molbev/msg234},
+ PMID = {12949130},
+ KEYWORDS = {bacterial phylogeny; maximum likelihood; quartet trees; lateral gene transfer}
+ }
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+ EDITOR = {Dayhoff, M. O.},
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+ at ARTICLE{debry2001,
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+ DOI = {10.1016/S1567-1348(03)00088-1},
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+
+ at ARTICLE{delarbre2001,
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+ DOI = {10.1007/s002390010250},
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+ }
+
+ at ARTICLE{delong2001,
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+ }
+
+ at ARTICLE{delsuc2001,
+ AUTHOR = {Delsuc, Fr{\'e}d{\'e}ric and Catzeflis, Fran\c{c}ois M. and Stanhope, Michael J. and Douzery, Emmanuel J. P.},
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+ TITLE = {The evolution of armadillos, anteaters and sloths depicted by nuclear and mitochondrial phylogenies: Implications for the status of the enigmatic fossil {Eurotamandua}},
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+ }
+
+ at ARTICLE{delsuc2002,
+ AUTHOR = {Delsuc, Fr{\'e}d{\'e}ric and Scally, Mark and Madsen, Ole and Stanhope, Michael J. and de Jong, Wilfried W. and Catzeflis, Fran\c{c}ois M. and Springer, Mark S. and Douzery, Emmanuel J. P.},
+ YEAR = 2002,
+ TITLE = {Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling on the Placental Tree Rooting},
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+ DOI = {},
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+ REMARK = {Suppl. Info.}
+ }
+
+ at ARTICLE{delsuc2003,
+ AUTHOR = {Delsuc, Fr{\'e}d{\'e}ric and Stanhope, Michael J. and Douzery, Emmanuel J. P.},
+ YEAR = 2003,
+ TITLE = {Molecular systematics of armadillos ({Xenarthra, Dasypodidae}): contribution of maximum likelihood and {Bayesian} analyses of mitochondrial and nuclear genes},
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+ PAGES = {261-275},
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+ }
+
+ at ARTICLE{delsuc2004,
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+ }
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+ at INCOLLECTION{desalle1994,
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+ AUTHOR = {Diaconis, Persi and Efron, Bradley},
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+
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+ AUTHOR = {van Dijk, Marjon A. M. and Madsen, Ole and Catzeflis, Fran\c{c}ois and Stanhope, Michael J. and de Jong, Wilfried W. and Pagel, Mark},
+ YEAR = 2001,
+ TITLE = {Protein sequence signatures support the African clade of mammals},
+ JOURNAL = {Proc. Natl. Acac. Sci. USA},
+ VOLUME = 98,
+ PAGES = {188-193},
+ PDF = {dijk2001.pnas.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {African mammals; Afrotheria}
+ }
+
+ at BOOK{dilba2003,
+ AUTHOR = {Dilba, Eberhard},
+ YEAR = 2003,
+ TITLE = {Typographie-Lexikon},
+ EDITION = 2,
+ PUBLISHER = {Eberhard Dilba Selbstverlag},
+ ADDRESS = {D\"usseldorf},
+ PDF = {books/dilba2003.typographie-lexikon.book.pdf},
+ KEYWORDS = {Typographie-Lexikon Lexikon und Lesebuch fuer alle, die mit Manuskript, Satz, Korrekturen, Typographie oder Buechern zu tun haben, fuer Autoren, Verlage, Werbeagenturen, Setzereien, Druckereien, oder fuer sonst Interessierte, mit etwa 700 Hauptstichwoertern und zahlreichen weiteren Begriffen, sowie einem interaktiven RGB-Farbmischer}
+ }
+
+ at ARTICLE{dimitropoulou2003,
+ AUTHOR = {Dimitropoulou, Polixeni and Cannings, Chris},
+ YEAR = 2003,
+ TITLE = {{RECSIM} and {INDSTATS}: probabilities of identity in general genealogies},
+ JOURNAL = {Bioinformatics},
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+ PAGES = {790-791},
+ PDF = {dimitropoulou2003.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg060},
+ PMID = {},
+ KEYWORDS = {}
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+
+ at ARTICLE{dimmic2002,
+ AUTHOR = {Dimmic, Matthew W. and Rest, Joshua S. and Mindell, David P. and Goldstein, Richard A.},
+ YEAR = 2002,
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+ PDF = {dimmic2002.jme.pdf},
+ DOI = {10.1007/s00239-001-2304-y},
+ PMID = {},
+ KEYWORDS = {General reversible transition Markov model, HIV, Lentivirus, Maximum likelihood method, Retroid, pol gene}
+ }
+
+ at ARTICLE{dixon1993,
+ AUTHOR = {Dixon, Michael T. and Hillis, David M.},
+ YEAR = 1993,
+ TITLE = {Ribosomal {RNA} Secondary Structure: Compensatory Mutations and Implicants for Phylogenetic Analysis},
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+ PDF = {dixon1993.mbe.pdf},
+ DOI = {},
+ PMID = {8450759},
+ KEYWORDS = {ribosomal RNA; secondary structure; phylogeny}
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+
+ at INPROCEEDINGS{dong2003,
+ AUTHOR = {Dong, Jian-xiong and Krzyzak, Adam and Suen, Ching Y.},
+ YEAR = 2003,
+ TITLE = {A Fast Parallel Optimization for Training Support Vector Machine},
+ BOOKTITLE = {Proceedings of the 3rd International Conference on Machine Learning and Data Mining in Pattern Recognition (MLDM 2003)},
+ PAGES = {96-105},
+ SERIES = {Lecture Notes in Computer Science},
+ VOLUME = {2734},
+ MONTH = {July},
+ PUBLISHER = {Springer},
+ ADDRESS = {Heidelberg},
+ PDF = {dong2003.lncs.pdf},
+ DOI = {},
+ PMID = {-},
+ KEYWORDS = {parallel computing;; SVM; support vector machines; training; parallel optimization}
+ }
+
+ at ARTICLE{doniger2002,
+ AUTHOR = {Doniger, Scott and Hofmann, Thomas and Yeh, Joanne},
+ YEAR = 2003,
+ TITLE = {Predicting {CNS} Permeability of Drug Molecules: Comparison of Neural Network and Support Vector Machine Algorithms},
+ JOURNAL = {J. Comput. Biol.},
+ VOLUME = 9,
+ PAGES = {849-864},
+ PDF = {doniger2002.jcb.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {neural net; support vector machine; machine-learning algorithms; blood brain barrier; central nervous system; predictive methods; kernel methods}
+ }
+
+ at ARTICLE{doolittle1999,
+ AUTHOR = {Doolittle, W. Ford},
+ YEAR = 1999,
+ TITLE = {Lateral Genomics},
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+ VOLUME = 24,
+ PAGES = {M5-M8},
+ NOTE = {Millenium Issue of TCB (9), TIBS (24), and TIG (15)},
+ PDF = {doolittle1999.tibs.pdf},
+ PDF = {doolittle1999.tcb.pdf},
+ PDF = {doolittle1999.tig.pdf},
+ DOI = {},
+ PMID = {10611671},
+ KEYWORDS = {}
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+ at ARTICLE{dopazo1993,
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+ at ARTICLE{dorman2002,
+ AUTHOR = {Dorman, Karin S. and Kaplan, Andrew H. and Sinsheimer, Janet S.},
+ YEAR = 2002,
+ TITLE = {Bootstrap Confidence Levels for {HIV-1} Recombination},
+ JOURNAL = {J. Mol. Evol.},
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+ DOI = {10.1007/s00239-001-0002-4},
+ PMID = {11821913},
+ KEYWORDS = {Bootstrapping; Confidence; Topol-ogy; Recombination; p-values; Accelerated bias-corrected percentile}
+ }
+
+ at INPROCEEDINGS{doroshenko1999,
+ AUTHOR = {Doroshenko, A. E. and Kononenko, I. S. and Korotun, A. Y.},
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+ TITLE = {A Coordination Model and Facilities for Efficient Parallel Computation},
+ BOOKTITLE = {Proceedings of the 5th International Conference on Parallel Computing Technologies (PaCT-99)},
+ SERIES = {Lecture Notes in Computer Science},
+ VOLUME = 1662,
+ PAGES = {42-47},
+ PUBLISHER = {Springer},
+ ADDRESS = {New York},
+ PDF = {doroshenko1999.LNCS.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel computing}
+ }
+
+ at ARTICLE{dosztanyi2001,
+ AUTHOR = {Doszt{\'a}nyi, Zsuzsanna and Torda, Andrew E.},
+ YEAR = 2001,
+ TITLE = {Amino acid similarity matrices based on force fields},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 17,
+ PAGES = {686-699},
+ PDF = {dosztanyi2001.bioinformatics.pdf},
+ DOI = {},
+ PMID = {11524370},
+ KEYWORDS = {Amino acid similarity matrices; force fields}
+ }
+
+ at ARTICLE{douady2003,
+ AUTHOR = {Douady, Christophe J. and Delsuc, Fr\'{e}d\'{e}ric and Boucher, Yan and Doolittle, W. Ford and Douzery, Emmanuel J. P.},
+ YEAR = 2003,
+ TITLE = {Comparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability},
+ JOURNAL = {Mol. Biol. Evol.},
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+ PAGES = {248-254},
+ PDF = {douady2003.mbe.pdf},
+ DOI = {10.1093/molbev/msg042},
+ PMID = {12598692},
+ KEYWORDS = {Bayesian; bootstrap; Markov chain Monte Carlo; maximum likelihood; phylogeny; posterior probability}
+ }
+
+ at ARTICLE{douady2003a,
+ AUTHOR = {Douady, Christophe J. and Dosay, Min\'{e} and Shivji, Mahmood S. and Stanhope, Michael J.},
+ YEAR = 2003,
+ TITLE = {Molecular phylogenetic evidence refuting the hypothesis of {Batoidea} (rays and skates) as derived sharks},
+ JOURNAL = {Mol. Phylogenet. Evol.},
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+ PAGES = {215-221},
+ PDF = {douady2003a.mpe.pdf},
+ DOI = {10.1016/S1055-7903(02)00333-0},
+ PMID = {},
+ REMARK = {interessant, sollte man mal reinschaun},
+ KEYWORDS = {}
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+ at ARTICLE{douglas1991,
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+ PDF = {hardcopy},
+ DOI = {},
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+ KEYWORDS = {Molecular phylogeny; Plastid; Algae; Plant; small subunit RNA}
+ }
+
+ at ARTICLE{dover2002,
+ AUTHOR = {Dover, Gabriel},
+ YEAR = 2002,
+ TITLE = {Molecular drive},
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+ PAGES = {587-589},
+ PDF = {dover2002.tig.pdf},
+ DOI = {10.1016/S0168-9525(02)02789-0},
+ PMID = {},
+ KEYWORDS = {Molecular drive; molecular evolution}
+ }
+
+ at ARTICLE{dowling2002,
+ AUTHOR = {Dowling, Ashley P. G.},
+ YEAR = 2002,
+ TITLE = {Testing the accuracy of {TreeMap} and {Brooks} parsimony analyses of coevolutionary patterns using artificial associations},
+ JOURNAL = {Cladistics},
+ VOLUME = 18,
+ PAGES = {416-435},
+ PDF = {dowling2002.cladistics.pdf},
+ DOI = {10.1016/S0748-3007(02)00007-5},
+ PMID = {},
+ KEYWORDS = {TreeMap; Brooks parsimony analyses; BPA}
+ }
+
+ at ARTICLE{dowling2003,
+ AUTHOR = {Dowling, Ashley P. G.},
+ YEAR = 2003,
+ TITLE = {Erratum to 'Testing the accuracy of {TreeMap} and {Brooks} parsimony analyses of coevolutionary patterns using artificial associations' [Cladistics 18 (2002) 416-435]},
+ JOURNAL = {Cladistics},
+ VOLUME = 19,
+ PAGES = {180},
+ PDF = {dowling2003.cladistics.pdf},
+ DOI = {10.1016/S0748-3007(03)00005-7},
+ PMID = {},
+ KEYWORDS = {Erratum; TreeMap; Brooks parsimony analyses; BPA},
+ REMARK = {Erratum to dowling2002}
+ }
+
+ at ARTICLE{dowton2002,
+ AUTHOR = {Dowton, Mark and Austin, Andrew D.},
+ YEAR = 2002,
+ TITLE = {Increased Congruence Does Not Necessarily Indicate Increased Phylogenetic Accuracy -- The Behavior of the Incongruence Length Difference Test in Mixed-Model Analyses},
+ JOURNAL = {Syst. Biol.},
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+ PAGES = {19-31},
+ PDF = {dowton2002.syst-biol.pdf},
+ DOI = {},
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+ KEYWORDS = {Incongruence; partition homogeneity; sensitivity analysis; simulated dataset; six-parameter parsimony}
+ }
+
+ at ARTICLE{drake1969,
+ AUTHOR = {Drake, J. W.},
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+ at ARTICLE{dress1996,
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+ PDF = {dress1996.discr-appl-math.pdf},
+ DOI = {},
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+ KEYWORDS = {}
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+
+ at ARTICLE{dress2000,
+ AUTHOR = {Dress, Andreas W. M. and Huber, K. T. and Moulton, V.},
+ YEAR = 2000,
+ TITLE = {An Exceptional Split Geometry},
+ JOURNAL = {Ann. Combin.},
+ VOLUME = 4,
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+ PMID = {},
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+ }
+
+ at ARTICLE{dress2001,
+ AUTHOR = {Dress, Andreas W. M. and Huber, K. T. and Moulton, V.},
+ YEAR = 2001,
+ TITLE = {Totally Split-Decomposable Metrics of Combinatorial Dimension Two},
+ JOURNAL = {Ann. Combin.},
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+ PDF = {dress2001.ann-combin.pdf},
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+ PMID = {},
+ KEYWORDS = {metric space, consistent metric, tight span, combinatorial dimension, Buneman com-plex, split system, compatibility, incompatibility, weakly compatible, 2-compatible, k-compatible, 3-crossfree}
+ }
+
+ at ARTICLE{drouin1999,
+ AUTHOR = {Drouin, Guy and Prat, Fr{\'e}d{\'e}ric and Ell, Michael and Clarke, G. D. Paul},
+ YEAR = 1999,
+ TITLE = {Detecting and Characterizing Gene Conversions Between Multigene Family Members},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 16,
+ PAGES = {1369-1390},
+ PDF = {drouin1999.mbe.pdf},
+ DOI = {},
+ PMID = {10563017},
+ KEYWORDS = {gene conversion; multigene families; Sawyer; co-double; SequEdit. on different regions of multigene family members}
+ }
+
+ at ARTICLE{drouin1995,
+ AUTHOR = {Drouin, G. and Moniz de S{/'a}, M. and Zuker, M.},
+ YEAR = 1995,
+ TITLE = {The {Giardia} lamblia actin gene and the phylogeny of the eukaryotes},
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+ PAGES = {841--849},
+ PDF = {NICHT VORHANDEN},
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+ at ARTICLE{drummond2001,
+ AUTHOR = {Drummond, Alexei and Rodrigo, Allen G.},
+ YEAR = 2001,
+ TITLE = {Reconstructing Genealogies of Serial Samples Under the Assumption of a Molecular Clock Using Serial-Sample UPGMA},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 18,
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+ PDF = {drummond2001.mbe.pdf},
+ DOI = {},
+ PMID = {11110896},
+ KEYWORDS = {longitudinal samples; serial samples; ancient DNA; phylogenetic reconstruction; UPGMA; sUPGMA}
+ }
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+ at ARTICLE{du1997,
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+ PMID = {-},
+ KEYWORDS = {parallel computing}
+ }
+
+ at ARTICLE{dunn2003,
+ AUTHOR = {Dunn, Katherine A. and McEachran, John D. and Honeycutt, Rodney L.},
+ YEAR = 2003,
+ TITLE = {Molecular phylogenetics of myliobatiform fishes ({Chondrichthyes}: {Myliobatiformes}), with comments on the effects of missing data on parsimony and likelihood},
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+ VOLUME = 27,
+ PAGES = {259-270},
+ PDF = {dunn2003.mpe.pdf},
+ DOI = {10.1016/S1055-7903(02)00442-6},
+ PMID = {},
+ REMARK = {interessant, sollte man mal reinschaun},
+ KEYWORDS = {Mitochondrial DNA; Myliobatiform fishes; Phylogeny; Missing data}
+ }
+
+ at ARTICLE{dunwell2001,
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+ PMID = {},
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+ at BOOK{durbin1998,
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+ }
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+ at ARTICLE{duret1994,
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+
+ at ARTICLE{durnford1999,
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+ PDF = {durnford1999.jme.pdf},
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+ PMID = {},
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+ }
+
+ at ARTICLE{dutheil2002,
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+ PAGES = {892-893},
+ PDF = {dutheil2002.bioinformatics.pdf},
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+
+ at ARTICLE{duvall1996,
+ AUTHOR = {Duvall, Melvin R. },
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+ at ARTICLE{duvall2001,
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+
+
+ at ARTICLE{ebedes2004,
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+ PDF = {ebedes2004.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/bth055},
+ PMID = {14764554},
+ KEYWORDS = {parallel computing; parallel bioinformatics; multiple sequence alignent;; workstation cluster}
+ }
+
+ at INPROCEEDINGS{eckstein1994,
+ AUTHOR = {Eckstein, Jonathan},
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+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel computing;; parallel mixed integer branch and bound}
+ }
+
+ at ARTICLE{edgar2003,
+ AUTHOR = {Edgar, Robert C. and Sj{\"o}lander, Kimmen},
+ YEAR = 2003,
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+ PAGES = {1404-1411},
+ PDF = {edgar2003.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg158},
+ PMID = {12874053},
+ KEYWORDS = {sequence alignment; tree reconstruction; HMM}
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+
+ at ARTICLE{edgar2004,
+ AUTHOR = {Edgar, Robert C. and Sj{\"o}lander, Kimmen},
+ YEAR = 2004,
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+ JOURNAL = {Bioinformatics},
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+ PDF = {edgar2004.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/bth090},
+ PMID = {14962936},
+ KEYWORDS = {scoring functions; protein sequence profile alignment}
+ }
+
+ at ARTICLE{edgar2004a,
+ AUTHOR = {Edgar, Robert C. and Sj{\"o}lander, Kimmen},
+ YEAR = 2004,
+ TITLE = {{COACH}: profile-profile alignment of protein families using hidden {Markov} models},
+ JOURNAL = {Bioinformatics},
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+ DOI = {10.1093/bioinformatics/bth091},
+ PMID = {14962937},
+ KEYWORDS = {profile alignment; protein sequence profile alignment; hidden Markov models; HMM}
+ }
+
+ at ARTICLE{edgell1998,
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+ at ARTICLE{edman1956a,
+ AUTHOR = {Edman, P.},
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+ AUTHOR = {Edman, P.},
+ TITLE = {Method for the determination of the protein sequence},
+ YEAR = 1970,
+ PAGES = {211-255},
+ EDITOR = {Needleman, S. B.},
+ BOOKTITLE = {Protein Sequence Determination},
+ PUBLISHER = {Springer Verlag},
+ ADDRESS = {Berlin},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at INCOLLECTION{edman1975,
+ AUTHOR = {Edman, P. and Henschen, A.},
+ TITLE = {Sequence Determination},
+ YEAR = 1975,
+ PAGES = {232-279},
+ EDITOR = {Needleman, S. B.},
+ BOOKTITLE = {Protein Sequence Determination: A sourcebook of methods and techniques},
+ PUBLISHER = {Springer Verlag},
+ ADDRESS = {Berlin},
+ EDITION = 2,
+ ISBN = {038707256X},
+ VOLUME = {8},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at INPROCEEDINGS{edmiston1987,
+ AUTHOR = {Edmiston, Elisabeth and Wagner, Robert A.},
+ YEAR = 1987,
+ TITLE = {Parallelization of the Dynamic Programming Algorithm for Comparison of Sequences},
+ PAGES = {78-80},
+ BOOKTITLE = {Proceedings of the 1987 International Conference on Parallel Processing},
+ PUBLISHER = {Penn State Press},
+ ADDRESS = {Pennsylvania},
+ PDF = {edmiston1987.Conf-Parall-Proc.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing; SIMD architecture}
+ }
+
+ at ARTICLE{edmiston1988,
+ AUTHOR = {Edmiston, E. and Wagner, R. A.},
+ YEAR = 1988,
+ TITLE = {Parallel processing of biological sequence comparison algorithms},
+ JOURNAL = {International Journal of Parallel Programming},
+ VOLUME = 17,
+ PAGES = {259-275},
+ PDF = {hardcopy, TODO; fernleihe, ULB, 7.7.2004},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing}
+ }
+
+ at ARTICLE{edwards1963,
+ AUTHOR = {Edwards A. W. F. , Cavalli-Sforza, L. L.},
+ YEAR = 1963,
+ TITLE = {The Reconstruction of Evolution (Abstract)},
+ JOURNAL = {Ann. Hum. Genet.},
+ VOLUME = 27,
+ PAGES = {104-105},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{edwards1963a,
+ AUTHOR = {Edwards A. W. F. , Cavalli-Sforza, L. L.},
+ YEAR = 1963,
+ TITLE = {The Reconstruction of Evolution (Abstract)},
+ JOURNAL = {Heredity},
+ VOLUME = 18,
+ PAGES = {553},
+ PDF = {hardcopy},
+ REMARK = {same as edwards1963},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at INCOLLECTION{edwards1964,
+ AUTHOR = {Edwards A. W. F. , Cavalli-Sforza, L. L.},
+ TITLE = {Reconstruction of evolutionary trees},
+ YEAR = 1964,
+ PAGES = {67-76},
+ EDITOR = {Heywood, V. H. and McNeill, J.},
+ BOOKTITLE = {Phenetic and Phylogenetic Classification},
+ PUBLISHER = {Systematics Association},
+ ADDRESS = {London, UK},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {},
+ REEMARK = {reprinted in: Cladistic Theory and Methodology, eds. T.Duncan and T.F.Stuessy. New York: Van Nostrand Reinhold (1985)}
+ }
+
+ at BOOK{edwards1972,
+ EDITOR = {Edwards A. W. F.},
+ YEAR = 1972,
+ TITLE = {Likelihood},
+ PUBLISHER = {Cambridge University Press},
+ ADDRESS = {Cambridge, UK},
+ ISBN = {},
+ KEYWORDS = {}
+ }
+
+ at BOOK{edwards1992,
+ EDITOR = {Edwards A. W. F.},
+ YEAR = 1992,
+ TITLE = {Likelihood},
+ PUBLISHER = {John Hopkins University Press},
+ ADDRESS = {Baltimore, USA},
+ ISBN = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{edwards2002,
+ AUTHOR = {Edwards, Scott V. and Boles, Walter E.},
+ YEAR = 2002,
+ TITLE = {Out of {Gondwana}: The origin of passerine birds},
+ JOURNAL = {TREE},
+ VOLUME = 17,
+ PAGES = {347-349},
+ PDF = {edwards2002.tree.pdf},
+ DOI = {10.1016/S0169-5347(02)02543-0},
+ PMID = {},
+ KEYWORDS = {RAG-1; c-mos; Gondwana; phylogeny; biogeography; c-myc; passerine; molecular clock}
+ }
+
+ at ARTICLE{eernisse1993,
+ AUTHOR = {Eernisse, Douglas and Kluge, Arnold G.},
+ YEAR = 1993,
+ TITLE = {Taxonomic Congruence versus Total Evidence, and Amniote Phylogeny Inferred from Fossils, Molecules, and Morphology},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 10,
+ PAGES = {1170-1195},
+ PDF = {eernisse1993.mbe.pdf},
+ DOI = {},
+ PMID = {8277850},
+ KEYWORDS = {phylogeny; classification; morphology; fossils; sequence alignment; rRNA; proteins; birds; mammals; total evidence; taxonomic congruence}
+ }
+
+ at ARTICLE{efron1975,
+ AUTHOR = {Efron, Bradley},
+ YEAR = 1975,
+ TITLE = {Defining the Curvature of a Statistical Problem (with Applications to Second Order Efficiency)},
+ JOURNAL = {Ann. Stat.},
+ VOLUME = 3,
+ PAGES = {1189-1242},
+ PDF = {efron1975.ann-stat.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Curvature; exponential families; Cramer-Rao lower bound; locally most powerful tests; Fisher information; second order efficiency; deficiency; maximum likelihood estimation}
+ }
+
+ at ARTICLE{efron1979,
+ AUTHOR = {Efron, Bradley},
+ YEAR = 1979,
+ TITLE = {Bootstrap methods: Another look at the Jackknife},
+ JOURNAL = {Ann. Stat.},
+ VOLUME = 7,
+ PAGES = {1-26},
+ PDF = {efron1979.ann-stat.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {jackknife; bootstrap; resampling; subsample values; nonparametric variance estimation; error rate estimation; discriminant analysis; nonlinear regression}
+ }
+
+ at ARTICLE{efron1981,
+ AUTHOR = {Efron, B. and Stein, C.},
+ YEAR = 1981,
+ TITLE = {The Jackknife Estimate of Variance},
+ JOURNAL = {Ann. Stat.},
+ VOLUME = 9,
+ PAGES = {586-596},
+ PDF = {efron1981.ann-stat.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Jackknife; variance estimation; ANOVA decomposition; bootstrap; U statistics}
+ }
+
+ at ARTICLE{efron1981a,
+ AUTHOR = {Efron, Bradley},
+ YEAR = 1981,
+ TITLE = {Maximum Likelihood and Decision Theory},
+ JOURNAL = {Ann. Stat.},
+ VOLUME = 10,
+ PAGES = {340-356},
+ PDF = {efron1981a.ann-stat.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Maximum likelihood estimate; summary; Fisher information; Stein estimation}
+ }
+
+ at ARTICLE{efron1986,
+ AUTHOR = {Efron, Bradley},
+ YEAR = 1986,
+ TITLE = {Discussion: Jackknife, Bootstrap and Other Resampling Methods in Regression Analysis},
+ JOURNAL = {Ann. Stat.},
+ VOLUME = 14,
+ PAGES = {1301-1304},
+ PDF = {efron1986.ann-stat.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{efron1996,
+ AUTHOR = {Efron, Bradley and Halloran, Elizabeth and Holmes, Susan},
+ YEAR = 1996,
+ TITLE = {Bootstrap confidence levels for phylogenetic trees},
+ JOURNAL = {Proc. Natl. Acad. Sci. USA},
+ VOLUME = 93,
+ PAGES = {13429-13434},
+ PDF = {efron1996.pnas.pdf},
+ DOI = {},
+ PMID = {8917608},
+ KEYWORDS = {Bootstrap confidence levels; Phylogenetic trees}
+ }
+
+ at ARTICLE{efron1996a,
+ AUTHOR = {Efron, Bradley and Halloran, Elizabeth and Holmes, Susan},
+ YEAR = 1996,
+ TITLE = {Bootstrap confidence levels for phylogenetic trees --- uncorrected Version},
+ JOURNAL = {Proc. Natl. Acad. Sci. USA},
+ VOLUME = 93,
+ PAGES = {7085-7090},
+ PDF = {efron1996a.pnas-uncorr.pdf},
+ DOI = {},
+ PMID = {8692949},
+ KEYWORDS = {Bootstrap confidence levels; Phylogenetic trees}
+ }
+
+ at ARTICLE{ehrenberg2003,
+ AUTHOR = {Ehrenberg, M{\aa}ns and Elf, Johan and Aurell, Erik and Sandberg, Rickard and Tegn{\'e}r, Jesper},
+ YEAR = 2003,
+ TITLE = {Systems Biology Is Taking Off},
+ JOURNAL = {Genome Res.},
+ VOLUME = 13,
+ PAGES = {2377-2380},
+ PDF = {ehrenberg2003.genome-res.pdf},
+ DOI = {10.1101/gr.1763203},
+ PMID = {},
+ KEYWORDS = {Systems Biology}
+ }
+
+ at ARTICLE{eicheler2004,
+ AUTHOR = {Eichler, Evan E. and Clark, Royden A. and She, Xinwei},
+ YEAR = 2004,
+ TITLE = {An Assessment of the Sequence Gaps: Unfinished Business in a Finished Human Genome},
+ JOURNAL = {Nat. Rev. Genet.},
+ VOLUME = 5,
+ PAGES = {345-354},
+ PDF = {eichler2004.nat-rev-genet.pdf},
+ DOI = {10.1038/nrg1322},
+ PMID = {},
+ KEYWORDS = {human genome; finished?}
+ }
+
+ at ARTICLE{eisen2003,
+ AUTHOR = {Eisen, Jonathan A. and Fraser, Claire M.},
+ YEAR = 2003,
+ TITLE = {Phylogenomics: Intersection of Evolution and Genomics},
+ JOURNAL = {Sience},
+ VOLUME = 300,
+ PAGES = {1706-1707},
+ PDF = {eisen2003.science.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Tree of Life; Phylogenomics; Evolution; Genomics}
+ }
+
+ at ARTICLE{eizirik2001,
+ AUTHOR = {Eizirik, E. and Murphy, W. J. and O'Brien, S. J.},
+ YEAR = 2001,
+ TITLE = {Molecular Dating and Biogeography of the Early Placental Mammal Radiation},
+ JOURNAL = {J. Hered.},
+ VOLUME = 92,
+ PAGES = {212-219},
+ PDF = {eizirik2001.j-hered.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Molecular Dating; Biogeography; Early Placental Mammals; Afrotheria; eutheria}
+ }
+
+ at ARTICLE{elemento2002,
+ AUTHOR = {Elemento, Olivier and Gascuel, Olivier and Lefranc, Marie-Paule},
+ YEAR = 2002,
+ TITLE = {Reconstructing the Duplication History of Tandemly Repeated Genes},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 19,
+ PAGES = {278-288},
+ PDF = {elemento2002.mbe.pdf},
+ DOI = {},
+ PMID = {11861887},
+ KEYWORDS = {Duplication History; Tandemly Repeated Genes}
+ }
+
+ at ARTICLE{elena2003,
+ AUTHOR = {Elena, Santiago F. and Lenski, Richard E.},
+ YEAR = 2003,
+ TITLE = {Microbial Genetics: Evolution Experiments with Microorganisms: The Dynamics and Genetic Bases of Adaptation},
+ JOURNAL = {Nat. Rev. Genet.},
+ VOLUME = 4,
+ PAGES = {4},
+ PDF = {elena2003.nrg.pdf},
+ DOI = {},
+ PMID = {},
+ REMARK = {interessant, sollte man mal reinschaun},
+ KEYWORDS = {Evolution Experiments; Microbial Genetics; Microorganisms; Adaptation}
+ }
+
+ at ARTICLE{elford1997,
+ AUTHOR = {Elford, Chris L. and Reed, Daniel A.},
+ YEAR = 1997,
+ TITLE = {Technology Trends and Disk Array Performance},
+ JOURNAL = {J. Parallel Distrib. Comput.},
+ VOLUME = 46,
+ PAGES = {136-147},
+ PDF = {elford1997.jpdc.pdf},
+ DOI = {10.1006/jpdc.1997.1405},
+ PMID = {-},
+ KEYWORDS = {parallel computing; Disk Array Performance}
+ }
+
+ at BOOK{eliason1993,
+ EDITOR = {Eliason, Scott R.},
+ YEAR = 1993,
+ TITLE = {Maximum Likelihood Estimation: Logic and Practice},
+ SERIES = {Quantitative Applications in the Social Sciences},
+ PUBLISHER = {Sage Publications},
+ ADDRESS = {Newbury Park},
+ ISBN = {0803941072},
+ KEYWORDS = {Maximum Likelihood in Social Sciences}
+ }
+
+ at ARTICLE{ellis2001,
+ AUTHOR = {Ellis, R. John},
+ YEAR = 2001,
+ TITLE = {Macromolecular crowding: Obvious but underappreciated},
+ JOURNAL = {TIBS},
+ VOLUME = 26,
+ PAGES = {597-604},
+ PDF = {ellis2001.tibs.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {protein complexes}
+ }
+
+ at ARTICLE{ellis2003,
+ AUTHOR = {Ellis, J. Christopher Ellis and Brown, James W.},
+ YEAR = 2003,
+ TITLE = {Genes within genes within bacteria},
+ JOURNAL = {Trends Biochem. Sci.},
+ VOLUME = 28,
+ PAGES = {521-523},
+ PDF = {ellis2003.tibs.pdf},
+ DOI = {10.1016/j.tibs.2003.08.002},
+ PMID = {},
+ KEYWORDS = {nested genes}
+ }
+
+ at BOOK{elrewini1994,
+ AUTHOR = {El-Rewini, Hesham and Lewis, Theodore G. and Ali, Hesham H.},
+ YEAR = 1994,
+ TITLE = {Task Scheduling in Parallel and Distributed Systems},
+ PUBLISHER = {Prentice-Hall},
+ ADDRESS = {Englewood Cliffs, New Jersey},
+ KEYWORDS = {Parallel Computing; Distributed Computing; Load Balancing; Scheduling}
+ }
+
+ at ARTICLE{elson2001,
+ AUTHOR = {Elson, J. L. and Andrews, R. M. and Chinnery, P. F. and Lightowlers, R. N. and Turnbull, D. M. and Howell, Neil},
+ YEAR = 2001,
+ TITLE = {Analysis of European mtDNAs for Recombination},
+ JOURNAL = {Am. J. Hum. Genet.},
+ VOLUME = 68,
+ PAGES = {145-153},
+ PDF = {elson2001.am-j-hum-genet.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Mitochondria; mtDNA; Recombination}
+ }
+
+ at INPROCEEDINGS{erdos1997,
+ AUTHOR = {Erd{\"o}s, P{\'e}ter L. and Steel, Michael A. and Sz{\'e}kely, L{'a}zl{\'o} A. and Warnow, Tandy J.},
+ YEAR = 1997,
+ TITLE = {Constructing Big Trees from Short Sequences},
+ PAGES = {827-837},
+ BOOKTITLE = {ICALP: 24th International Colloquium on Automata, Languages and Programming},
+ EDITOR = {Degano, Pierpaolo and Gorrieri, Robert and Marchetti-Spaccamela, Alberto},
+ PUBLISHER = {Springer-Verlag},
+ VOLUME = {1256},
+ SERIES = {Lecture Notes in Computer Science},
+ PDF = {erdos1997.lncs-manuscr.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{erdos1997a,
+ AUTHOR = {Erd{\"o}s, P{\'e}ter L. and Steel, Michael A. and Sz{\'e}kely, L{'a}zl{\'o} A. and Warnow, Tandy J.},
+ YEAR = 1997,
+ TITLE = {Local Quartet Splits of a Binary Tree Infer All Quartet Splits via one Dyadic Inference Rule},
+ JOURNAL = {Comput. Artif. Intell.},
+ VOLUME = 16,
+ PAGES = {217-227},
+ PDF = {erdos1997a.comput-artif-intell.ps},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{erdos1999,
+ AUTHOR = {Erd{\"o}s, P{\'e}ter L. and Steel, Michael A. and Sz{\'e}kely, L{'a}zl{\'o} A. and Warnow, Tandy J.},
+ YEAR = 1999,
+ TITLE = {A Few Logs Suffice to Build (Almost) All Trees (I)},
+ JOURNAL = {Random Struct. Algorithms},
+ VOLUME = 14,
+ PAGES = {153-184},
+ PDF = {erdos1999.random-struct-algorithms.pdf},
+ DOI = {10.1002/(SICI)1098-2418(199903)14:2<153::AID-RSA3>3.0.CO;2-R},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{erdos1999a,
+ AUTHOR = {Erd{\"o}s, P{\'e}ter L. and Steel, Michael A. and Sz{\'e}kely, L{'a}zl{\'o} A. and Warnow, Tandy J.},
+ YEAR = 1999,
+ TITLE = {A Few Logs Suffice to Build (Almost) All Trees: Part {II}},
+ JOURNAL = {Theor. Comp. Sci.},
+ VOLUME = 221,
+ PAGES = {77-118},
+ PDF = {erdos1999.theor-comp-sci.pdf},
+ KEYWORDS = {Phylogeny; Evolutionary tree reconstruction; Distance-based methods; Quartet methods; Short quartet methods; Dyadic closure method; Witness-antiwitness method}
+ }
+
+ at ARTICLE{emmert1994,
+ AUTHOR = {Emmert, D. B. and Stoehr, P. J. and Stoesser, G. and Cameron, G. N.},
+ YEAR = 1994,
+ TITLE = {The {European} {Bioinformatics} {Institute} ({EBI}) databases},
+ JOURNAL = {Nucleic Acids Res.},
+ VOLUME = 22,
+ PAGES = {3445-3449},
+ PDF = {NICHT VORHANDEN},
+ DOI = {},
+ PMID = {7937043},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{eskin2003,
+ AUTHOR = {Eskin, Eleazar and Stafford Noble, William and Singer, Yoram},
+ YEAR = 2003,
+ TITLE = {Using Substitution Matrices to Estimate Probability Distributions for Biological Sequences},
+ JOURNAL = {J. Comput. Biol.},
+ VOLUME = 9,
+ PAGES = {775-792},
+ PDF = {eskin2003.jcb.pdf},
+ DOI = {10.1089/10665270260518263},
+ PMID = {},
+ KEYWORDS = {substitution matrix-based probability estimation methods; Bayesian interpretation; large alphabets; protein families; protein classification}
+ }
+
+ at ARTICLE{estrada2002,
+ AUTHOR = {Estrada, Ernesto},
+ YEAR = 2002,
+ TITLE = {Characterization of the folding degree of proteins},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 18,
+ PAGES = {697-704},
+ PDF = {estrada2002.bioinformatics.pdf},
+ DOI = {},
+ PMID = {12050066},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{eulenstein1997,
+ AUTHOR = {Eulenstein, Oliver and Mirkin, Boris and Vingron, Martin},
+ YEAR = 1997,
+ TITLE = {Comparison of Annotation Duplication, Tree Mapping, and Copying as Methods to Compare Gene Trees with Species Trees},
+ JOURNAL = {DIMACS Series in Discrete Mathematics and Theoretical Computer Sciences},
+ VOLUME = 37,
+ PAGES = {71-93},
+ PDF = {eulenstein1997.DIMACS-manuscr.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Duplication; Tree Mapping; Gene Trees; Species Trees}
+ }
+
+ at ARTICLE{eulenstein1998,
+ AUTHOR = {Eulenstein, Oliver and Vingron, Martin},
+ YEAR = 1998,
+ TITLE = {On the Equivalence of Two Tree Mapping Measures},
+ JOURNAL = {Discr. Appl. Math.},
+ VOLUME = 88,
+ PAGES = {103-128},
+ PDF = {eulenstein1998.discr-appl-math.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{eulenstein2004,
+ AUTHOR = {Eulenstein, Oliver and Chen, Duhong and Burleigh, J. Gordon and Fern{\'a}ndez-Baca, David and Sanderson, Michael J.},
+ YEAR = 2004,
+ TITLE = {Performance of Flip Supertree Construction with a Heuristic Algorithm},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 53,
+ PAGES = {299-308},
+ PDF = {eulenstein2004.syst-biol.pdf},
+ DOI = {10.1080/10635150490423719},
+ PMID = {},
+ KEYWORDS = {supertree;; MRF; Flipping; phylogeny; simulation study; supertree}
+ }
+
+ at BOOK{ewens2001,
+ AUTHOR = {Ewens, Warren J. and Grant, Gregory R.},
+ YEAR = 2001,
+ TITLE = {Statistical Methods in Bioinformatics: An Introduction},
+ PUBLISHER = {Springer Verlag},
+ ADDRESS = {New York, USA},
+ ISBN = {0-387-95229-2},
+ KEYWORDS = {Bioinformatics; Statistical Methods}
+ }
+
+ at ARTICLE{eyre1998,
+ AUTHOR = {Eyre-Walker, Adam},
+ YEAR = 1998,
+ TITLE = {Problems with Parsimony in Sequences of Biased Base Composition},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 47,
+ PAGES = {686-690},
+ PDF = {eyre1998.jme.pdf},
+ DOI = {},
+ PMID = {9847410},
+ KEYWORDS = {parsimony; G+C content; GC content; base composition; mutation pattern}
+ }
+
+ at ARTICLE{eyre2001,
+ AUTHOR = {Eyre-Walker, Adam and Awadalla, Philip},
+ YEAR = 2001,
+ TITLE = {Does Human {mtDNA} Recombine?},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 53,
+ PAGES = {430-435},
+ PDF = {eyre2001.jme.pdf},
+ DOI = {10.1007/s002390010232},
+ PMID = {11675602},
+ KEYWORDS = {Recombination; Mitochondria; Human genetics; Human evolution; mtDNA}
+ }
+
+
+ at ARTICLE{faivovich2002,
+ AUTHOR = {Faivovich, Juli{\'a}n},
+ YEAR = 2002,
+ TITLE = {On {RASA}},
+ JOURNAL = {Cladistics},
+ VOLUME = 18,
+ PAGES = {324-333},
+ PDF = {faivovich2002.cladistics.pdf},
+ DOI = {10.1006/clad.2002.0205},
+ PMID = {},
+ KEYWORDS = {Relative Apparent Synapomorphy Analysis (RASA); "optimal" outgroups; find long branches; eliminate long-branch attraction}
+ }
+
+ at TECHREPORT{farach1993,
+ AUTHOR = {Farach, Martin and Kannan, Sampath and Warnow, Tandy},
+ YEAR = 1993,
+ MONTH = {April},
+ TITLE = {A Robust Model for Finding Optimal Evolutionary Trees},
+ INSTITUTION = {DIMACS},
+ ADDRESS = {Rudgers, NJ, USA},
+ TYPE = {DIMACS Technical Report},
+ NUMBER = {93-22},
+ PDF = {farach1993.DIMACS93-22.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fares2002,
+ AUTHOR = {Fares, Mario A. and Elena, Santiago F. and Ortiz, Javier and Moya, Andr\'{e}s and Barrio, Eladio},
+ YEAR = 2002,
+ TITLE = {A Sliding Window-Based Method to Detect Selective Constraints in Protein-Coding Genes and Its Application to {RNA} Viruses},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 55,
+ PAGES = {509-521},
+ PDF = {fares2002.jme.pdf},
+ DOI = {10.1007/s00239-002-2346-9},
+ PMID = {},
+ KEYWORDS = {FMDV; HIV-1; positive selection; selective constraints; structural/functional domains; window-based method}
+ }
+
+ at ARTICLE{farris2002,
+ AUTHOR = {Farris, James S.},
+ YEAR = 2002,
+ TITLE = {{RASA} Attributes Highly Significant Structure to Randomized Data},
+ JOURNAL = {Cladistics},
+ VOLUME = 18,
+ PAGES = {334-353},
+ PDF = {farris2002.cladistics.pdf},
+ DOI = {10.1006/clad.2002.0204},
+ PMID = {},
+ KEYWORDS = {Relative Apparent Synapomorphy Analysis (RASA); relative apparent similarity analysis}
+ }
+
+ at ARTICLE{fast2002,
+ AUTHOR = {Fast, Naomi M. and Xue, Lingru and Bingham, Scott and Keeling, Patrick J.},
+ YEAR = 2002,
+ TITLE = {Re-examining Alveolate Evolution Using Multiple Protein Molecular Phylogenies},
+ JOURNAL = {J. Eukaryot. Microbiol.},
+ VOLUME = 49,
+ PAGES = {30-37},
+ PDF = {fast2002.j-eukaryot-microbiol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Actin; Apicomplexa; ciliates; dinoflagellates; evolution; heat shock protein; tubulin; significant outgroup effect on topology; combined data; puzzle}
+ }
+
+ at INPROCEEDINGS{fatourou2003,
+ AUTHOR = {Fatourou, Panagiota and Spirakis, Paul},
+ YEAR = 2003,
+ TITLE = {A New Scheduling Algorithm for General Strict Multithreaded Computations},
+ BOOKTITLE = {Proceedings of the 13th International Symposium on Distributed Computing (DISC 1999)},
+ PAGES = {312-326},
+ SERIES = {Lecture Notes in Computer Science},
+ VOLUME = {1693},
+ MONTH = {September},
+ PUBLISHER = {Springer},
+ ADDRESS = {Berlin Heidelberg},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {scheduling; parallel computing; work-stealing paradigm; execution time; space complexity; communication cost; fully strict multithreaded computations}
+ }
+
+ at ARTICLE{faty2002,
+ AUTHOR = {Faty, Mahamadou and Fink, Michel and Barral, Yves},
+ YEAR = 2002,
+ TITLE = {Septins: A ring to part mother and daughter},
+ JOURNAL = {Curr. Genet.},
+ VOLUME = 41,
+ PAGES = {123-131},
+ PDF = {faty2002.curr-genet.pdf},
+ DOI = {10.1007/s00294-002-0304-0},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fedorov1998,
+ AUTHOR = {Alexey Fedorov and Larisa Fedorova and Valery Starshenko and Vadim Filatov and Eugeni Grigor'ev},
+ YEAR = 1998,
+ TITLE = {Influence of Exon Duplication on Intron and Exon Phase Distribution},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 46,
+ PAGES = {263-271},
+ PDF = {fedorov1998.jme.pdf},
+ DOI = {},
+ PMID = {9493351},
+ KEYWORDS = {Human genes; Exon/Intron gene structure; Intron phase order; Exon shuffling; Gene evolution}
+ }
+
+ at ARTICLE{fedorov1999,
+ AUTHOR = {Fedorov, Alexey N. and Fedorova, Larisa V. and Grechko, Vernata V. and Ryabinin, Dmitrii M. and Sheremet'eva, Valentina A. and Bannikova, Anna A. and Lomov, Alexei A. and Ryskov, Alexei P. and Darevsky, Ilya S.},
+ YEAR = 1999,
+ TITLE = {Variable and Invariable {DNA} Repeat Characters Revealed by Taxonprint Approach Are Useful for Molecular Systematics},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 48,
+ PAGES = {69-76},
+ PDF = {fedorov1999.jme.pdf},
+ DOI = {},
+ PMID = {9873078},
+ KEYWORDS = {DNA repeats; DNA restriction fragment analysis; Taxonprint; Molecular systematics; Lacertidae; Primates}
+ }
+
+ at ARTICLE{fedorov2003,
+ AUTHOR = {Fedorov, Alexei and Roy, Scott and Fedorova, Larisa and Gilbert, Walter},
+ YEAR = 2003,
+ TITLE = {Mystery of Intron Gain},
+ JOURNAL = {Genome Res.},
+ VOLUME = 13,
+ PAGES = {2236-2241},
+ PDF = {fedorov2003.genome-res.pdf},
+ DOI = {10.1101/gr.1029803},
+ PMID = {12975308},
+ KEYWORDS = {intron; intron gain; intron transposition}
+ }
+
+ at ARTICLE{felsenstein1973,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1973,
+ TITLE = {Maximum Likelihood and Minimum--Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters},
+ JOURNAL = {Syst. Zool.},
+ VOLUME = 22,
+ PAGES = {240-249},
+ PDF = {felsenstein1973.syst-zool.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {evolutionary trees; maximum likelihood; minimum steps method}
+ }
+
+ at ARTICLE{felsenstein1978,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1978,
+ TITLE = {The number of evolutionary trees},
+ JOURNAL = {Syst. Zool.},
+ VOLUME = 27,
+ PAGES = {27-33},
+ PDF = {felsenstein1978.syst-zool.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Evolutionary Trees, Cladistic Methods, Combinatorial Algorithms, Graphs}
+ }
+
+ at ARTICLE{felsenstein1978a,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1978,
+ TITLE = {Cases in which Parsimony or Compatibility Methods Will be Positively Misleading},
+ JOURNAL = {Syst. Zool.},
+ VOLUME = 27,
+ PAGES = {401-410},
+ PDF = {felsenstein1978a.syst-zool.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Numerical Cladistics, Phylogenetic Inference, Maximum Likelihood Estimation, Parsimony, Compatibility}
+ }
+
+ at ARTICLE{felsenstein1979,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1979,
+ TITLE = {Alternative Methods of Phylogenetic Inference and their Interrelationship},
+ JOURNAL = {Syst. Zool.},
+ VOLUME = 28,
+ PAGES = {49-62},
+ PDF = {felsenstein1979.syst-zool.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Statistical inference; phylogenies; numerical cladistics; maximum likelihood estimation}
+ }
+
+ at ARTICLE{felsenstein1981,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1981,
+ TITLE = {Evolutionary trees from {DNA} sequences: a maximum likelihood approach},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 17,
+ PAGES = {368-376},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {7288891},
+ KEYWORDS = {evolution; phylogeny; maximum likelihood; parsimony; estimation; DNA sequences}
+ }
+
+ at ARTICLE{felsenstein1982,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1982,
+ TITLE = {Numerical Methods for Inferring Evolutionary Trees},
+ JOURNAL = {Q. Rev. Biol.},
+ VOLUME = 57,
+ PAGES = {379-404},
+ PDF = {felsenstein1982.q-rev-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{felsenstein1983,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1983,
+ TITLE = {Statistical Inference of Phylogenies},
+ JOURNAL = {J. Royal Statist. Soc. A},
+ VOLUME = 146,
+ PAGES = {246-272},
+ PDF = {felsenstein1983.r-stat-soc-a.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {phylogeny; evolution; estimation; numerical taxonomy; systematics; branching Markov processes; maximum likelihood; parsimony; nucleic acids; clustering}
+ }
+
+ at ARTICLE{felsenstein1983a,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1983,
+ TITLE = {Parsimony in Systematics: Biological and Statistical Issues},
+ JOURNAL = {Annu. Rev. Ecol. Syst.},
+ VOLUME = 14,
+ PAGES = {313-333},
+ PDF = {felsenstein1983a.annu-rev-ecol-syst.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{felsenstein1984,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1984,
+ TITLE = {Distance methods for inferring phylogenies: A Justification},
+ JOURNAL = {Evolution},
+ VOLUME = 38,
+ PAGES = {16-24},
+ PDF = {felsenstein1984.evol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{felsenstein1985,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1985,
+ TITLE = {Confidence Limits on Phylogenies: An Approach Using the Bootstrap},
+ JOURNAL = {Evolution},
+ VOLUME = 39,
+ PAGES = {783-791},
+ PDF = {felsenstein1985.evol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{felsenstein1985a,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1985,
+ TITLE = {Phylogenies and the Comparative Method},
+ JOURNAL = {Am. Nat.},
+ VOLUME = 125,
+ PAGES = {1-15},
+ PDF = {felsenstein1985a.am-nat.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{felsenstein1985b,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1985,
+ TITLE = {Phylogenies from Gene Frequencies: A Statistical Problem},
+ JOURNAL = {Syst. Zool.},
+ VOLUME = 34,
+ PAGES = {300-311},
+ PDF = {felsenstein1985b.syst-zool.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Phylogenies, Statistical Inference, Gene Frequencies, Electrophoretic Polymorphisms, Genetic Distances}
+ }
+
+ at ARTICLE{felsenstein1985c,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1985,
+ TITLE = {Confidence Limits on Phylogenies with a Molecular Clock},
+ JOURNAL = {Syst. Zool.},
+ VOLUME = 34,
+ PAGES = {154-161},
+ PDF = {felsenstein1985c.syst-zool.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Phylogenies, Confidence Limits, Molecular Clock, Statistical Inference, Hypothesis Testing}
+ }
+
+ at ARTICLE{felsenstein1986,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1986,
+ TITLE = {Discussion: Jackknife, Bootstrap and Other Resampling Methods in Regression Analysis},
+ JOURNAL = {Ann. Stat.},
+ VOLUME = 14,
+ PAGES = {1304-1305},
+ PDF = {felsenstein1986.ann-stat.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{felsenstein1988,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1988,
+ TITLE = {Phylogenies from molecular sequences: Inference and reliability},
+ JOURNAL = {Annu. Rev. Genet.},
+ VOLUME = 22,
+ PAGES = {521-565},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{felsenstein1989,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1989,
+ TITLE = {{PHYLIP} -- {P}hylogeny {I}nference {P}ackage (Version 3.2)},
+ JOURNAL = {Cladistics},
+ VOLUME = 5,
+ PAGES = {164-166},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at MANUAL{felsenstein1990,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1990,
+ TITLE = {{PHYLIP} manual, version 3.3},
+ ORGANIZATION = {University of Washington},
+ ADDRESS = {Seattle}
+ }
+
+ at MANUAL{felsenstein1993,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1993,
+ TITLE = {{PHYLIP} manual, version 3.5},
+ ORGANIZATION = {Department of Genetics, University of Washington},
+ ADDRESS = {Seattle}
+ }
+
+ at MANUAL{felsenstein1993a,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1993,
+ TITLE = {{PHYLIP} ({P}hylogeny {I}nference {P}ackage) version 3.5c},
+ ORGANIZATION = {Department of Genetics, University of Washington},
+ ADDRESS = {Seattle},
+ NOTE = {Distributed by the author}
+ }
+
+ at ARTICLE{felsenstein1993b,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1993,
+ TITLE = {Is There Something Wrong with the Bootstrap on Phylogenies? (A Reply to Hillis and Bull)},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 42,
+ PAGES = {193-200},
+ PDF = {felsenstein1993b.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{felsenstein1996,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1996,
+ TITLE = {Inferring Phylogenies from Protein Sequences by Parsimony, Distance, and Likelihood Methods},
+ JOURNAL = {Methods Enzymol.},
+ VOLUME = 266,
+ PAGES = {418-427},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {8743697},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{felsenstein1996a,
+ AUTHOR = {Felsenstein, Joseph and Churchill, Gary A.},
+ YEAR = 1996,
+ TITLE = {A Hidden Markov Model Approach to Variation Among Sites in Rate of Evolution},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 13,
+ PAGES = {93-104},
+ PDF = {felsenstein1996a.mbe.pdf},
+ DOI = {},
+ PMID = {8583911},
+ KEYWORDS = {likelihood; phylogeny; statistical inference; Hidden Marcov Model; rate of evolution; molecular sequences}
+ }
+
+ at ARTICLE{felsenstein1997,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 1997,
+ TITLE = {An Alternating Least Squares Approach to Inferring Phylogenies from Pairwise Distances},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 46,
+ PAGES = {101-111},
+ PDF = {felsenstein1997.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Alternating Least Squares, Distance Methods, Fitch-Margoliash Method, Phylogenies}
+ }
+
+ at ARTICLE{felsenstein2001,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 2001,
+ TITLE = {The Troubled Growth of Statistical Phylogenetics},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 50,
+ PAGES = {465-467},
+ PDF = {felsenstein2001.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Statistical Phylogenetics}
+ }
+
+ at ARTICLE{felsenstein2001a,
+ AUTHOR = {Felsenstein, Joseph},
+ YEAR = 2001,
+ TITLE = {Taking Variation of Evolutionary Rates Between Sites into Account in Inferring Phylogenies},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 53,
+ PAGES = {447-455},
+ PDF = {felsenstein2001a.jme.pdf},
+ DOI = {10.1007/s002390010234},
+ PMID = {11675604},
+ KEYWORDS = {Phylogeny; Evolutionary rate; Maximum likelihood; Distance; Parsimony; Invariants}
+ }
+
+ at BOOK{felsenstein2003,
+ AUTHOR = {Felsenstein, Joe},
+ YEAR = 2004,
+ TITLE = {Infering Phylogenies},
+ PUBLISHER = {Sinauer Associates},
+ ADDRESS = {Sunderland, Massachusetts},
+ ISBN = {0878931775},
+ REMARK = {felsenstein2003 = felsenstein2004; the book was in the shops in 2003, official date 2004},
+ KEYWORDS = {Infering Phylogenies; Phylogenetic Methods}
+ }
+
+ at BOOK{felsenstein2004,
+ AUTHOR = {Felsenstein, Joe},
+ YEAR = 2004,
+ TITLE = {Infering Phylogenies},
+ PUBLISHER = {Sinauer Associates},
+ ADDRESS = {Sunderland, Massachusetts},
+ ISBN = {0878931775},
+ REMARK = {felsenstein2003 = felsenstein2004; the book was in the shops in 2003, official date 2004},
+ KEYWORDS = {Infering Phylogenies; Phylogenetic Methods}
+ }
+
+ at ARTICLE{feng1997,
+ AUTHOR = {Feng, Da-Fei and Doolittle, Russell F.},
+ YEAR = 1997,
+ TITLE = {Converting Amino Acid Alignment Scores into Measures of Evolutionary Time: A Simulation Study of Various Relationships},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 44,
+ PAGES = {361-370},
+ PDF = {feng1997.jme.pdf},
+ DOI = {},
+ PMID = {9089075},
+ KEYWORDS = {Alignment scores; Distance measures; Substitution tables}
+ }
+
+ at ARTICLE{feng2003,
+ AUTHOR = {Feng, Xizhou and Buell, Duncan A. and Rose, John R. and Waddell, Peter J.},
+ YEAR = 2003,
+ TITLE = {Parallel algorithms for Bayesian phylogenetic inference},
+ JOURNAL = {J. Parallel Distrib. Comput.},
+ VOLUME = 63,
+ PAGES = {707-718},
+ PDF = {feng2003.jpdc.pdf},
+ DOI = {10.1016/S0743-7315(03)00079-0},
+ PMID = {},
+ KEYWORDS = {parallel computing; parallel bioinformatics;; Phylogenetic inference; MCMC; Distributed parallel computation}
+ }
+
+ at ARTICLE{ferrari2003,
+ AUTHOR = {Ferrari, Carlo and Guerra, Concettina and Zanotti, Giuseppe},
+ YEAR = 2003,
+ TITLE = {A grid-aware approach to protein structure comparison},
+ JOURNAL = {J. Parallel Distrib. Comput.},
+ VOLUME = 63,
+ PAGES = {728-737},
+ PDF = {ferrari2003.jpdc.pdf},
+ DOI = {10.1016/S0743-7315(03)00081-9},
+ PMID = {},
+ KEYWORDS = {parallel computing; parallel bioinformatics;; protein structure comparison; grid computing}
+ }
+
+ at ARTICLE{field1988,
+ AUTHOR = {Field, Kathrine G. and Olsen, Gary J. and Lane, David J. and Giovannoni, Stephen J. and Ghiselin, Michael T. and Raff, Elizabeth C. and Pace, Norman R. and Raff, Rudolf A.},
+ YEAR = 1988,
+ TITLE = {Molecular Phylogeny of the Animal Kingdom},
+ JOURNAL = {Sciene},
+ VOLUME = 239,
+ PAGES = {748-753},
+ PDF = {field1988.science.pdf},
+ DOI = {},
+ PMID = {3277277},
+ KEYWORDS = {Animal Kingdom; Metazoa; molecular phylogeny; 18S rRNA}
+ }
+
+ at ARTICLE{finarelli2002,
+ AUTHOR = {Finarelli, John A. and Clyde, William C.},
+ YEAR = 2002,
+ TITLE = {Comparing the Gap Excess Ratio and the Retention Index of the Stratigraphic Character},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 51,
+ PAGES = {166-176},
+ PDF = {finarelli2002.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Gap Excess Ratio; GER; Retention Index; RI; Stratigraphic Character}
+ }
+
+ at ARTICLE{finden1985,
+ AUTHOR = {Finden, C. R. and Gordon, A. D.},
+ YEAR = 1985,
+ TITLE = {Obtaining common pruned trees},
+ JOURNAL = {J. Classif.},
+ VOLUME = 2,
+ PAGES = {255-276},
+ PDF = {NICHT VORHANDEN, TODO, ULB: 61 # 1.1984 - 14.1997 # Standort: > LS / bib z j 360 <},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {consensus; trees; common pruned trees}
+ }
+
+ at ARTICLE{finkelstein1998,
+ AUTHOR = {Finkelstein, Mark and Fitch, Walter M. and Lanciani, Carmine A. and Miyamoto, Michael M.},
+ YEAR = 1998,
+ TITLE = {Estimating the Probabilities of Runs of Identical Events Within Biological Sequences},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 15,
+ PAGES = {470-472},
+ PDF = {finkelstein1998.mbe.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {run probabilities; biological sequences; covarion hypothesis; superoxide dismutase}
+ }
+
+ at ARTICLE{fisher1912,
+ AUTHOR = {Fisher, R. A.},
+ YEAR = 1912,
+ TITLE = {On an absolute criterion for fitting frequency curves},
+ JOURNAL = {Messenger in Mathematics},
+ VOLUME = 41,
+ PAGES = {155-160},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ REMARKS = {introducing maximum likelihood method},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fisher1922,
+ AUTHOR = {Fisher, R. A.},
+ YEAR = 1922,
+ TITLE = {On the mathematical foundations of theoretical statistics},
+ JOURNAL = {Phil. Trans. Royal Soc. London A},
+ VOLUME = 222,
+ PAGES = {309-368},
+ PDF = {fisher1922.phil-trans-rsoc-london-a.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fisher1928,
+ AUTHOR = {Fisher, R. A.},
+ YEAR = 1928,
+ TITLE = {The General Sampling Distribution of the Multiple Correlation Coefficient},
+ JOURNAL = {Phil. Trans. Royal Soc. London A},
+ VOLUME = 121,
+ PAGES = {654-673},
+ PDF = {fisher1928.phil-trans-rsoc-london-a.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fisher1929,
+ AUTHOR = {Fisher, R. A.},
+ YEAR = 1929,
+ TITLE = {Tests of Significance in Harmonic Analysis},
+ JOURNAL = {Phil. Trans. Royal Soc. London A},
+ VOLUME = 125,
+ PAGES = {54-59},
+ PDF = {fisher1929.phil-trans-rsoc-london-a.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fisher1930,
+ AUTHOR = {Fisher, R. A.},
+ YEAR = 1930,
+ TITLE = {The Moments of the Distribution for Normal Samples of Measures of Departure from Normality},
+ JOURNAL = {Phil. Trans. Royal Soc. London A},
+ VOLUME = 130,
+ PAGES = {16-28},
+ PDF = {fisher1930.phil-trans-rsoc-london-a.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fisher1934,
+ AUTHOR = {Fisher, R. A.},
+ YEAR = 1934,
+ TITLE = {Probability Likelihood and Quantity of Information in the Logic of Uncertain Inference},
+ JOURNAL = {Phil. Trans. Royal Soc. London A},
+ VOLUME = 146,
+ PAGES = {1-8},
+ PDF = {fisher1934.phil-trans-rsoc-london-a.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fisher1934a,
+ AUTHOR = {Fisher, R. A.},
+ YEAR = 1934,
+ TITLE = {Two New Properties of Mathematical Likelihood},
+ JOURNAL = {Phil. Trans. Royal Soc. London A},
+ VOLUME = 144,
+ PAGES = {285-307},
+ PDF = {fisher1934a.phil-trans-rsoc-london-a.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fisher1936,
+ AUTHOR = {Fisher, R. A.},
+ YEAR = 1936,
+ TITLE = {The Use of Multiple Measurements in Taxonomic Problems},
+ JOURNAL = {Annals of Eugenics},
+ VOLUME = 7,
+ PAGES = {179-188},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fisher1950,
+ AUTHOR = {Fisher, R. A.},
+ YEAR = 1950,
+ TITLE = {A Class of Enumerations of Importance in Genetics},
+ JOURNAL = {Phil. Trans. Royal Soc. London B},
+ VOLUME = 136,
+ PAGES = {509-520},
+ PDF = {fisher1950.phil-trans-rsoc-london-b.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fitch1967,
+ AUTHOR = {Fitch, Walter M. and Margoliash, Emanuel},
+ YEAR = 1967,
+ TITLE = {Construction of Phylogenetic Trees},
+ JOURNAL = {Science},
+ VOLUME = 155,
+ PAGES = {279-284},
+ PDF = {fitch1967.science.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fitch1970,
+ AUTHOR = {Fitch, Walter M.},
+ YEAR = 1970,
+ TITLE = {Distinguishing Homologous from Analogous Proteins},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 19,
+ PAGES = {99-113},
+ PDF = {fitch1970.syst-zool.pdf},
+ DOI = {},
+ PMID = {5449325},
+ KEYWORDS = {Homologous Proteins; Homologous Proteins}
+ }
+
+ at ARTICLE{fitch1971,
+ AUTHOR = {Fitch, W. M.},
+ TITLE = {Toward defining the course of evolution: {M}inimum change for a specific tree topology},
+ YEAR = 1971,
+ JOURNAL = {Syst. Zool.},
+ VOLUME = 20,
+ PAGES = {406-416},
+ PDF = {fitch1971.syst-zool.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fitch1977,
+ AUTHOR = {Fitch, Walter M.},
+ YEAR = 1977,
+ TITLE = {On the problem of discovering the most parsimonious tree},
+ JOURNAL = {Am. Nat.},
+ VOLUME = 111,
+ PAGES = {99-113},
+ PDF = {fitch1977.am-nat.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {most parsimonious tree}
+ }
+
+ at ARTICLE{fitch1981,
+ AUTHOR = {Fitch, Walter M.},
+ TITLE = {A Non-Sequential Method for Constructing Trees and Hierarchical Classifications},
+ YEAR = 1981,
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 18,
+ PAGES = {30-37},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {7334526},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fitch1982,
+ AUTHOR = {Fitch, Walter M. and Smith, Temple F.},
+ YEAR = 1982,
+ TITLE = {Implications of Minimal Length Trees},
+ JOURNAL = {Syst. Zool.},
+ VOLUME = 31,
+ PAGES = {68-75},
+ PDF = {fitch1982.syst-zool.pdf},
+ DOI = {},
+ PMID = {},
+ REMARK = {Commented by hendy1983, mcmorris1983},
+ KEYWORDS = {minimal trees; Hamiltonian circuits; evolutionary rates; maximum parsimony}
+ }
+
+ at ARTICLE{fitch1983,
+ AUTHOR = {Fitch, Walter M. and Smith, Temple F.},
+ YEAR = 1983,
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+ DOI = {},
+ PMID = {},
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+ }
+
+ at ARTICLE{fitch1986,
+ AUTHOR = {Fitch, Walter M.},
+ TITLE = {The Estimate of Total Nucleotide Substitutions from Pairwise Differences is Biased},
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+ KEYWORDS = {}
+ }
+
+ at ARTICLE{fitch1995,
+ AUTHOR = {Fitch, W. M.},
+ TITLE = {Uses for Evolutionary Trees},
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+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
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+ at ARTICLE{fitch1997,
+ AUTHOR = {Fitch, Walter M.},
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+ DOI = {},
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+ }
+
+ at ARTICLE{fitch2000,
+ AUTHOR = {Fitch, Walter M.},
+ YEAR = 2000,
+ TITLE = {Homology -- a personal view on some of the problems},
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+ DOI = {},
+ PMID = {},
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+ }
+
+ at ARTICLE{fitch2000,
+ AUTHOR = {Fitch, Walter M. and Bush, Robin M. and Bender, Catherine A. and Subbarao, Kanta and Cox, Nancy J.},
+ YEAR = 2000,
+ TITLE = {Predicting the Evolution of {Human Influenza A}},
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+
+ at ARTICLE{fitch2003,
+ AUTHOR = {Fitch, B. G. and Germain, R. S. and Mendell, M. and Pitera, J. and Pitman, M. and Rayshubskiy, A. and Sham, Y. and Suits, F. and Swope, W. and Ward, T. J. C. and Zhestkov, Y. and Zhou, R.},
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+ }
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+ at PHDTHESIS{fleissner2003,
+ AUTHOR = {Flei{\ss}ner, Roland},
+ YEAR = 2003,
+ TITLE = {Sequence alignment and phylogenetic inference},
+ SCHOOL = {Heinrich-Heine-Universit{\"a}t D{\"u}sseldorf},
+ ADDRESS = {D{\"u}sseldorf, Germany},
+ PDF = {fleissner2003.phdthesis.pdf},
+ DOI = {},
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+ at ARTICLE{florea1998,
+ AUTHOR = {Florea, Liliana and Hartzell, George and Zhang, Zheng and Rubin, Gerald M. and Webb Miller},
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+ at ARTICLE{fornasari2002,
+ AUTHOR = {Fornasari, Maria Silvina and Parisi, Gustavo and Echave, Julian},
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+ TITLE = {Site-Specific Amino Acid Replacement Matrices from Structurally Constrained Protein Evolution Simulations},
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+ DOI = {},
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+ at ARTICLE{forst2001,
+ AUTHOR = {Forst, Christian V. and Schulten, Klaus},
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+ at BOOK{foster1995,
+ AUTHOR = {Foster, Ian},
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+ TITLE = {Designing and Building Parallel Programs: Concepts and Tools for Parallel Software Engineering},
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+
+ at ARTICLE{foster1999,
+ AUTHOR = {Foster, Peter G. and Hickey, Donal A.},
+ YEAR = 1999,
+ TITLE = {Compositional Bias May Affect Both {DNA}-Based and Protein-Based Phylogenetic Reconstructions},
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+ at ARTICLE{foster2001,
+ AUTHOR = {Foster, James A.},
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+ at MISC{foster2001a,
+ AUTHOR = {Foster, Peter G.},
+ YEAR = 2001,
+ MONTH = {July},
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+ NOTE = {},
+ PDF = {foster2001a.idiots.pdf},
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+ KEYWORDS = {}
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+ at ARTICLE{foster2001b,
+ AUTHOR = {Foster, Peter and Torroni, Antonio and Renfrew, Colin and R{\"o}hl, Arne},
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+ TITLE = {Phylogenetic Star Contraction Applied to Asian and Papuan mtDNA Evolution},
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+ }
+
+ at ARTICLE{foulds1982,
+ AUTHOR = {Foulds, L. R. and Graham, R. L.},
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+ at ARTICLE{foulkes2004,
+ AUTHOR = {Foulkes, Andrea S. and De Gruttola, Victor},
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+
+ at ARTICLE{freedman1986,
+ AUTHOR = {Freedman, D. A.},
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+ at ARTICLE{freeling2001,
+ AUTHOR = {Freeling, Michael},
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+ at ARTICLE{friedman2001,
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+ AUTHOR = {Friedman, Nir and Ninio, Matan and Pe'er, Itsik and Pupko, Tal},
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+ at ARTICLE{friesen1997,
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+ at BOOK{frisch1991,
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+ at ARTICLE{fu1997,
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+ at ARTICLE{fu2001,
+ AUTHOR = {Fu, Yun--Xin},
+ YEAR = 2001,
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+ at ARTICLE{fukami1991,
+ AUTHOR = {Fukami--Kobayashi, Kaoru and Tateno, Yoshio},
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+ at BOOK{futuyma1986,
+ AUTHOR = {Futuyma, Douglas J.},
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+ at BOOK{futuyma1990,
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+ KEYWORDS = {chimpanzee; bonobo; genetic diversity; non-recombining region of the Y-chromosome (NRY); coalescence}
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+ at ARTICLE{garcia1997,
+ AUTHOR = {Garcia-Dorado, Aurora},
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+ }
+
+ at BOOK{garey1979,
+ AUTHOR = {Garey, M. and Johnson, D. S.},
+ YEAR = 1979,
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+
+ at ARTICLE{garnieldien2002,
+ AUTHOR = {Gamieldien, Junaid and Ptitsyn, Andrey and Hide, Winston},
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+ TITLE = {Eukaryotic genes in {Mycobacterium tuberculosis} could have a role in pathogenesis and immunomodulation},
+ JOURNAL = {Trends Genet.},
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+ KEYWORDS = {Eukaryotic genes; Mycobacterium tuberculosis}
+ }
+
+ at ARTICLE{gascuel1997,
+ AUTHOR = {Gascuel, Olivier},
+ YEAR = 1997,
+ TITLE = {{BIONJ}: An Improved Version of the {NJ} Algorithm Based on a Simple Model of Sequence Data},
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+ PAGES = {685-695},
+ PDF = {gascuel1997.mbe.pdf},
+ DOI = {},
+ PMID = {9254330},
+ KEYWORDS = {phylogeny; neighbor-joining; distance method; model of data; variances and covariances of distance estimates}
+ }
+
+ at ARTICLE{gascuel2001,
+ AUTHOR = {Gascuel, Olivier and Bryant, David and Denis, Fran\c{c}ois},
+ YEAR = 2001,
+ TITLE = {Strengths and Limitations of the Minimum Evolution Principle},
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+ PAGES = {621-627},
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+ }
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+ at ARTICLE{gascuel2003,
+ AUTHOR = {Gascuel, Olivier and Hendy, Michael D. and Jean-Marie, Alain and McLachlan, Robert},
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+ DOI = {10.1080/10635150390132821},
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+ KEYWORDS = {Asymptotic enumeration; random generation; recognition; recursion; tandem duplication trees}
+ }
+
+ at ARTICLE{gatesy2002,
+ AUTHOR = {Gatesy, John and Matthee, Conrad and DeSalle, Rob and Hayashi, Cheryl},
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+ TITLE = {Resolution of a Supertree/Supermatrix Paradox},
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+ PAGES = {652-664},
+ PDF = {gatesy2002.syst-biol.pdf},
+ DOI = {10.1080/10635150290102311},
+ PMID = {},
+ KEYWORDS = {supertree; Supertree/Supermatrix Paradox}
+ }
+
+ at ARTICLE{gatesy1999,
+ AUTHOR = {Gatesy, John and O'Grady, Patrick and Baker, Richard H.},
+ YEAR = 1999,
+ TITLE = {Corroboration among Data Sets in Simultaneous Analysis: Hidden Support for Phylogenetic Relationships among Higher Level Artiodactyl Taxa},
+ JOURNAL = {Cladistics},
+ VOLUME = 15,
+ PAGES = {271-313},
+ PDF = {gatesy1999.cladistics.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{gatesy2001,
+ AUTHOR = {Gatesy, J. and O'Leary, M. A.},
+ YEAR = 2001,
+ TITLE = {Deciphering whale origins with molecules and fossils},
+ JOURNAL = {TREE},
+ VOLUME = 16,
+ PAGES = {562-570},
+ PDF = {gatesy2001.tree.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Cetacea; whale; phylogeny; missing data; fossil; macroevolution; Artiodactyla; cladistics; palaeontology}
+ }
+
+ at ARTICLE{gatesy2001err,
+ AUTHOR = {Gatesy, J. and O'Leary, M. A.},
+ YEAR = 2001,
+ TITLE = {Deciphering whale origins with molecules and fossils: Erratum},
+ JOURNAL = {TREE},
+ VOLUME = 16,
+ PAGES = {658},
+ PDF = {gatesy2001err.tree.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Cetacea; whale; phylogeny; missing data; fossil; macroevolution; Artiodactyla; cladistics; palaeontology}
+ }
+
+ at ARTICLE{gatesy2004,
+ AUTHOR = {Gatesy, John and Baker, Richard H. and Hayashi, Cheryl},
+ YEAR = 2004,
+ TITLE = {Inconsistencies in Arguments for the Supertree Approach: Supermatrices versus Supertrees of {Crocodylia}},
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+ PAGES = {342-355},
+ PDF = {gatesy2004.syst-biol.pdf},
+ DOI = {10.1080/10635150490423971},
+ PMID = {},
+ KEYWORDS = {supertree; supermatrix; total evidence;; Inconsistencies; Supermatrices; Supertree; Crocodylia}
+ }
+
+ at BOOK{gauss1880,
+ AUTHOR = {Gauss, Carl Friedrich},
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+ TITLE = {Werke in 12 B\"anden},
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+ ADDRESS = {G{\"o}ttingen},
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+ at INCOLLECTION{gauss1821,
+ AUTHOR = {Gauss, Carl Friedrich},
+ YEAR = 1821,
+ TITLE = {Theoria combinationis observationum erroribus minimis obnoxiae (pars prior)},
+ PAGES = {3-26},
+ SERIES = {Werke},
+ BOOKTITLE = {Wahrscheinlichkeitsrechnung und Geometrie},
+ VOLUME = 4,
+ PUBLISHER = {Dieterichsche Universit{\"a}ts-Druckerei},
+ ADDRESS = {G{\"o}ttingen},
+ PDF = {gauss1821.werke-4.3-26.pdf},
+ DOI = {},
+ PMID = {},
+ NOTE = {reprinted 1873 from \emph{Commentationes societatis regiae scientiarium Gottingensis recentiores}, 15. Feb. 1821},
+ KEYWORDS = {}
+ }
+
+ at INCOLLECTION{gauss1821a,
+ AUTHOR = {Gauss, Carl Friedrich},
+ TITLE = {{Anzeigen eigner Abhandlungen}: Theoria combinationis observationum erroribus minimis obnoxiae (pars prior)},
+ YEAR = 1821,
+ PAGES = {95-100},
+ SERIES = {Werke},
+ BOOKTITLE = {Wahrscheinlichkeitsrechnung und Geometrie},
+ VOLUME = 4,
+ PUBLISHER = {Dieterichsche Universit{\"a}ts-Druckerei},
+ ADDRESS = {G{\"o}ttingen},
+ PDF = {gauss1821a.werke-4.95-100.pdf},
+ DOI = {},
+ PMID = {},
+ NOTE = {reprinted 1873 from \emph{G{\"o}ttinginsche gelehrte Anzeigen}, 26. Feb. 1821},
+ KEYWORDS = {}
+ }
+
+ at INCOLLECTION{gauss1823,
+ AUTHOR = {Gauss, Carl Friedrich},
+ YEAR = 1823,
+ TITLE = {Theoria combinationis observationum erroribus minimis obnoxiae (pars posterior)},
+ PAGES = {27-54},
+ SERIES = {Werke},
+ BOOKTITLE = {Wahrscheinlichkeitsrechnung und Geometrie},
+ VOLUME = 4,
+ PUBLISHER = {Dieterichsche Universit{\"a}ts-Druckerei},
+ ADDRESS = {G{\"o}ttingen},
+ PDF = {gauss1823.werke-4.27-54.pdf},
+
+ DOI = {},
+ PMID = {},
+ NOTE = {reprinted 1873 from \emph{Commentationes societatis regiae scientiarium Gottingensis recentiores}, 2. Feb. 1823},
+ KEYWORDS = {}
+ }
+
+ at INCOLLECTION{gauss1823a,
+ AUTHOR = {Gauss, Carl Friedrich},
+ YEAR = 1823,
+ TITLE = {{Anzeigen eigner Abhandlungen}: Theoria combinationis observationum erroribus minimis obnoxiae (pars posterior)},
+ PAGES = {100-104},
+ EDITOR = {},
+ SERIES = {Werke},
+ BOOKTITLE = {Wahrscheinlichkeitsrechnung und Geometrie},
+ VOLUME = 4,
+ PUBLISHER = {Dieterichsche Universit{\"a}ts-Druckerei},
+ ADDRESS = {G{\"o}ttingen},
+ PDF = {gauss1823a.werke-4.100-104.pdf},
+ DOI = {},
+ PMID = {},
+ NOTE = {reprinted 1873 from \emph{G{\"o}ttinginsche gelehrte Anzeigen}, 26. Feb. 1823},
+ KEYWORDS = {}
+ }
+
+ at INCOLLECTION{gauss1826,
+ AUTHOR = {Gauss, Carl Friedrich},
+ YEAR = 1826,
+ TITLE = {Supplementum Theoriae combinationis observationum erroribus minimis obnoxiae},
+ PAGES = {55-94},
+ SERIES = {Werke},
+ BOOKTITLE = {Wahrscheinlichkeitsrechnung und Geometrie},
+ VOLUME = 4,
+ PUBLISHER = {Dieterichsche Universit{\"a}ts-Druckerei},
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+ KEYWORDS = {Polya theory; random graphs; structural isomers}
+ }
+
+ at ARTICLE{goldman1990,
+ AUTHOR = {Goldman, Nick},
+ YEAR = 1990,
+ TITLE = {Maximum likelihood inference of phylogenetic trees, with special reference to a poisson process model of {DNA} substitution and to parsimony analyses},
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+ PDF = {goldman1990.syst-zool.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{goldman1993,
+ AUTHOR = {Goldman, Nick},
+ YEAR = 1993,
+ TITLE = {Statistical tests of models of {DNA} substitution},
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+ VOLUME = 36,
+ PAGES = {182-198},
+ PDF = {hardcopy},
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+ }
+
+ at ARTICLE{goldman1993a,
+ AUTHOR = {Goldman, Nick},
+ YEAR = 1993,
+ TITLE = {Simple diagnostic statistical tests of models for {DNA} substitution},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 37,
+ PAGES = {650-661},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {8114118},
+ KEYWORDS = {phylogenetic inference; evolutionary models; statistical testing; hypothesis testing; constant sites; invariant sites; selection}
+ }
+
+ at ARTICLE{goldman1994,
+ AUTHOR = {Goldman, Nick and Yang, Ziheng},
+ YEAR = 1994,
+ TITLE = {A Codon--based Model of Nucleotide Substitution for Protein--coding {DNA} Sequences},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 11,
+ PAGES = {725-736},
+ PDF = {goldman1994.mbe.pdf},
+ DOI = {},
+ PMID = {7968486},
+ KEYWORDS = {models; nonsynonymous substitution; nucleotide substitution; phylogenetic estimation; protein-coding sequences; synonymous substitution}
+ }
+
+ at ARTICLE{goldman2000,
+ AUTHOR = {Goldman, Nick and Whelan, Simon},
+ YEAR = 2000,
+ TITLE = {Statistical Tests of Gamma-Distributed Rate Heterogeneity in Models of Sequence Evolution in Phylogenetics},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 17,
+ PAGES = {975-978},
+ PDF = {goldman2000.mbe.pdf},
+ DOI = {},
+ PMID = {10833204},
+ KEYWORDS = {likelihood ratio tests; gamma distribution; maximum likelihood; model comparison; molecular evolution; phylogenetics}
+ }
+
+ at ARTICLE{goldman2000a,
+ AUTHOR = {Goldman, Nick and Anderson, Jon P. and Rodrigo, Allen G.},
+ YEAR = 2000,
+ TITLE = {Likelihood-Based Tests of Topologies in Phylogenetics},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 49,
+ PAGES = {652-670},
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+ DOI = {},
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+ KEYWORDS = {Kishino-Hasegawa test; maximum likelihood; phylogeny; Shimodaira-Hasegawa test; statistical tests; tree topology}
+ }
+
+ at ARTICLE{goldman2002,
+ AUTHOR = {Goldman, Nick and Whelan, Simon},
+ YEAR = 2002,
+ TITLE = {A Novel Use of Equilibrium Frequencies in Models of Sequence Evolution},
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+ PDF = {goldman2002.mbe.pdf},
+ DOI = {},
+ PMID = {},
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+ }
+
+ at ARTICLE{goloboff1996,
+ AUTHOR = {Goloboff, Pablo A.},
+ YEAR = 1996,
+ TITLE = {Methods for Faster Parsimony Analysis},
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+ PAGES = {199-220},
+ PDF = {goloboff1996.cladistics.pdf},
+ DOI = {10.1006/clad.1996.0015},
+ PMID = {},
+ KEYWORDS = {algorithm; fast parsimony analysis; speedup}
+ }
+
+ at ARTICLE{goloboff1999,
+ AUTHOR = {Goloboff, Pablo A.},
+ YEAR = 1999,
+ TITLE = {Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima},
+ JOURNAL = {Cladistics},
+ VOLUME = 15,
+ PAGES = {415-428},
+ PDF = {goloboff1999.cladistics.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Large Data Sets; Composite Optima}
+ }
+
+ at ARTICLE{goloboff2002,
+ AUTHOR = {Goloboff, Pablo A.},
+ YEAR = 2002,
+ TITLE = {Optimization of Polytomies: State Set and Parallel Operations},
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+ PAGES = {269-275},
+ PDF = {goloboff2002.mpe.pdf},
+ DOI = {10.1006/mpev.2001.1049},
+ PMID = {11820847},
+ KEYWORDS = {parallel bioinformatics; parallel computing; parsimony; Fitch parsimony; state set}
+ }
+
+ at ARTICLE{goloboff2002b,
+ AUTHOR = {Goloboff, Pablo A. and Pol, Diego},
+ YEAR = 2002,
+ TITLE = {Semi-strict supertrees},
+ JOURNAL = {Cladistics},
+ VOLUME = 18,
+ PAGES = {514-525},
+ PDF = {goloboff2002a.cladistics.pdf},
+ DOI = {10.1016/S0748-3007(02)00117-2},
+ PMID = {},
+ KEYWORDS = {supertrees; semi-strict supertrees; matrix representation method}
+ }
+
+ at ARTICLE{goloboff2003,
+ AUTHOR = {Goloboff, Pablo A. and Farris, James S. and K{\"a}llersj{\"o}, Mari and Oxelman, Bengt and Ram{\'i}rez, Mart{\'i}n J. and Szumik, Claudia A.},
+ YEAR = 2003,
+ TITLE = {Improvements to resampling measures of group support},
+ JOURNAL = {Cladistics},
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+ PAGES = {324-332},
+ PDF = {goloboff2003.cladistics.pdf},
+ DOI = {10.1016/S0748-3007(03)00060-4},
+ PMID = {},
+ KEYWORDS = {assessment of group support; resampling methods; bootstrapping; jackknifing; symmetric resampling}
+ }
+
+ at ARTICLE{goloboff2003a,
+ AUTHOR = {Goloboff, Pablo A.},
+ YEAR = 2003,
+ TITLE = {Parsimony, likelihood, and simplicity},
+ JOURNAL = {Cladistics},
+ VOLUME = 19,
+ PAGES = {91-103},
+ PDF = {goloboff2003a.cladistics.pdf},
+ DOI = {10.1016/S0748-3007(03)00017-3},
+ PMID = {},
+ KEYWORDS = {Parsimony; likelihood; very complex models; very simple models; estimating many parameters; }
+ }
+
+ at ARTICLE{golovljova2002,
+ AUTHOR = {Golovljova, Irina and Brus-Sj\"{o}lander, Katarina and Lindegren, Gunnel and Vene, Sirkka and Vasilenko, Veera and Plyusnin, Alexander and Lundkvist, {\AA}ke},
+ YEAR = 2002,
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+ DOI = {10.1002/jmv.10231},
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+ }
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+ at ARTICLE{gontcharov2004,
+ AUTHOR = {Gontcharov, Andrey A. and Marin, Birger and Melkonian, Michael},
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+ PAGES = {612-624},
+ PDF = {gontcharov2004.mbe.pdf},
+ DOI = {10.1093/molbev/msh052},
+ PMID = {14739253},
+ KEYWORDS = {Combined analyses; phylogeny; rbcL; SSU rDNA; Streptophyta; Zygnematophyceae}
+ }
+
+ at ARTICLE{gonzales2002,
+ AUTHOR = {Gonzales, Matthew J. and Dugan, Jonathan M. and Shafer, Robert W.},
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+ PAGES = {54-59},
+ PUBLISHER = {Springer},
+ ADDRESS = {New York},
+ PDF = {gorbunova1999.LNCS.pdf},
+ DOI = {},
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+ KEYWORDS = {parallel computing; Kirdin kinetic machine; Kinetic Model; Parallel Data Processing; heap encoding}
+ }
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+ at ARTICLE{gordon1986,
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+
+ at ARTICLE{goremykin2003,
+ AUTHOR = {Goremykin, Vadim V. and Hirsch-Ernst, Karen I. and W{\"o}lfl, Stefan and Hellwig, Frank H.},
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+ TITLE = {Analysis of the {Amborella trichopoda} Chloroplast Genome Sequence Suggests That {Amborella} Is Not a Basal Angiosperm},
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+ PAGES = {1499-1505},
+ PDF = {goremykin2003.mbe.pdf},
+ DOI = {10.1093/molbev/msg159},
+ PMID = {12832641},
+ KEYWORDS = {Amborella; chloroplast genomes; angiosperms; gymnosperms; molecular evolution; substitution rates}
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+ at ARTICLE{gotoh1996,
+ AUTHOR = {Gotoh, Osamu},
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+ at ARTICLE{gower1996,
+ AUTHOR = {Gower, David J. and Wilkinson, Mark},
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+ AUTHOR = {Gouy, Manolo and Li, Wen--Hsiung},
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+ AUTHOR = {Grant, Taran and Kluge, Arnold G.},
+ YEAR = 2003,
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+ DOI = {},
+ PMID = {9066792},
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+ }
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+ at ARTICLE{grassly1999,
+ AUTHOR = {Grassly, Nicholas C. and Harvey, Paul H. and Holmes, Edward C.},
+ YEAR = 1999,
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+ }
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+ KEYWORDS = {molecular timescales of evolution; precision; chicken}
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+ }
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+ at ARTICLE{green2002,
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+ at ARTICLE{gregory2003,
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+ DOI = {10.1016/S0168-9525(03)00192-6},
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+ KEYWORDS = {indel bias; genome size}
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+ at ARTICLE{grice1997,
+ AUTHOR = {Grice, J. Alicia and Hughey, Richard and Speck, Don},
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+ at ARTICLE{grishin1995,
+ AUTHOR = {Grishin, Nick V.},
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+ at ARTICLE{grishin1999,
+ AUTHOR = {Grishin, Nick V.},
+ YEAR = 1999,
+ TITLE = {A Novel Approach to Phylogeny Reconstruction from Protein Sequences},
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+ at BOOK{gropp1994,
+ AUTHOR = {Gropp, William and Lusk, Ewing and Skjellum, Anthony},
+ YEAR = 1994,
+ TITLE = {Using {MPI}},
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+ ADDRESS = {Cambridge, Massachusetts}
+ }
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+ at BOOK{gropp1998,
+ AUTHOR = {Gropp, William and Huss--Lederman, Steven and Lumsdaine, Andrew and Lusk, Ewing and Nitzberg, Bill and Saphir, William and Snir, Marc},
+ YEAR = 1998,
+ TITLE = {{MPI}: The Complete Reference - The {MPI} Extensions},
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+ EDITION = 2,
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+ at BOOK{gropp1999,
+ AUTHOR = {Gropp, William and Lusk, Ewing and Thakur, Rajeev},
+ YEAR = 1999,
+ TITLE = {Using {MPI}: Portable Parallel Programming with the Message-Passing Interface},
+ EDITION = 2,
+ PUBLISHER = {The MIT Press},
+ ADDRESS = {Cambridge, Massachusetts},
+ ISBN = {0262571323},
+ KEYWORDS = {parallel computing; programming; MPI; Message Passing Interface}
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+ at BOOK{gropp1999a,
+ AUTHOR = {Gropp, William and Lusk, Ewing and Thakur, Rajeev},
+ YEAR = 1999,
+ TITLE = {Using {MPI-2}: Advanced Features of the Message-Passing Interface},
+ EDITION = 2,
+ PUBLISHER = {The MIT Press},
+ ADDRESS = {Cambridge, Massachusetts},
+ ISBN = {0262571331},
+ KEYWORDS = {parallel computing; programming; MPI-2; Message Passing Interface}
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+ at ARTICLE{gruenenfelder2002,
+ AUTHOR = {Gr\"{u}nenfelder, Bj\"{o}n and Winzeler, Elizabeth A.},
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+ at ARTICLE{gu1995,
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+ at ARTICLE{gu1998,
+ AUTHOR = {Gu, Xun and Li, Wen-Hsiung},
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+ }
+
+ at ARTICLE{gu2001,
+ AUTHOR = {Gu, Xun},
+ YEAR = 2001,
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+ VOLUME = 18,
+ PAGES = {453-464},
+ PDF = {gu2001.mbe.pdf},
+ DOI = {},
+ PMID = {11264396},
+ KEYWORDS = {gene family evolution; functional divergence; gene (genome) duplication; maximum likelihood; functional prediction}
+ }
+
+ at ARTICLE{gu2002,
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+ DOI = {},
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+ at ARTICLE{guigo1996,
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+ at ARTICLE{guindon2002,
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+ DOI = {},
+ PMID = {11919295},
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+ at ARTICLE{guindon2003,
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+ at INPROCEEDINGS{gpwg2000,
+ AUTHOR = {{Grass Phylogeny Working Group}},
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+ at ARTICLE{gpwg2001,
+ AUTHOR = {{Grass Phylogeny Working Group}},
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+ at ARTICLE{haeseler1993a,
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+ PMID = {15014142},
+ REMARK = {erratum for Table 2 under hanada2004err},
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+ at ARTICLE{hanada2004err,
+ AUTHOR = {Hanada, Kousuke and Suzuki, Yoshiyuki and Gojobori, Takashi},
+ YEAR = 2004,
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+ YEAR = 2003,
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+ PDF = {huelsenbeck1997b.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Felsenstein Zone; insect phylogeny; long-branch attraction; neighbor joining; parsimony}
+ }
+
+ at ARTICLE{huelsenbeck1998,
+ AUTHOR = {Huelsenbeck, John P.},
+ YEAR = 1998,
+ TITLE = {Systematic Bias in Phylogenetic Analysis: Is the Strepsiptera Problem Solved?},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 47,
+ PAGES = {519-537},
+ PDF = {pov1998.syst-biol-47.3.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Systematic Bias; Phylogenetic Analysis; Strepsiptera}
+ }
+
+ at ARTICLE{huelsenbeck1999,
+ AUTHOR = {Huelsenbeck, John P. and Nielsen, Rasmus},
+ YEAR = 1999,
+ TITLE = {Variation in the Pattern of Nucleotide Substitution Across Sites},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 48,
+ PAGES = {86-93},
+ PDF = {huelsenbeck1999.jme.pdf},
+ DOI = {},
+ PMID = {9873080},
+ KEYWORDS = {likelihood-ratio testing; maximum likelihood; molecular evolution; molecular systematics; phylogeny}
+ }
+
+ at ARTICLE{huelsenbeck2000,
+ AUTHOR = {Huelsenbeck, John P. and Rannala, Bruce and Larget, Bret},
+ YEAR = 2000,
+ TITLE = {A Bayesian Framework for the Analysis of Cospeciation},
+ JOURNAL = {Evolution},
+ VOLUME = 54,
+ PAGES = {352-364},
+ PDF = {huelsenbeck2000.evolution.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Cospeciation; host switching; Markov chain Monte Carlo; molecular biology; molecular evolution; phylogeny}
+ }
+
+ at ARTICLE{huelsenbeck2001,
+ AUTHOR = {Huelsenbeck, John P. and Ronquist, Fredrik},
+ YEAR = 2001,
+ TITLE = {{MRBAYES}: Bayesian inference of phylogenetic trees},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 17,
+ PAGES = {754-755},
+ PDF = {huelsenbeck2001.bioinformatics.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Bayesian inference; phylogenetic trees}
+ }
+
+ at ARTICLE{huelsenbeck2001a,
+ AUTHOR = {Huelsenbeck, John P. and Ronquist, Fredrik and Nielsen, Rasmus and Bollback, Jonathan P.},
+ YEAR = 2001,
+ TITLE = {Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology},
+ JOURNAL = {Science},
+ VOLUME = 294,
+ PAGES = {2310-2314},
+ PDF = {huelsenbeck2001a.science.pdf,huelsenbeck2001a.science-suppl.pdf},
+ DOI = {},
+ PMID = {11743192},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{huelsenbeck2002,
+ AUTHOR = {Huelsenbeck, John P.},
+ YEAR = 2002,
+ TITLE = {Testing a Covariotide Model of {DNA} Substitution},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 19,
+ PAGES = {698-707},
+ PDF = {huelsenbeck2002.mbe.pdf},
+ DOI = {},
+ PMID = {11961103},
+ KEYWORDS = {covarion-covariotide model; integrated likelihood; likelihood ratio; Markov chain Monte Carlo; maximum likelihood; mixed chi-square}
+ }
+
+ at ARTICLE{huelsenbeck2002a,
+ AUTHOR = {Huelsenbeck, John P. and Imennov, Nikita S.},
+ YEAR = 2002,
+ TITLE = {Geographic Origin of Human Mitochondrial {DNA}: Accommodating Phylogenetic Uncertainty and Model Comparison},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 51,
+ PAGES = {155-165},
+ PDF = {huelsenbeck2002a.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Human Origin; Mitochondrial DNA; Phylogenetic Uncertainty; Model Comparison; MCMC}
+ }
+
+ at ARTICLE{huelsenbeck2002b,
+ AUTHOR = {Huelsenbeck, John P. and Larget, Bret and Miller, Richard and Ronquist, Fredrik},
+ YEAR = 2002,
+ TITLE = {Potential Applications and Pitfalls of {Bayesian} Inference of Phylogeny},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 51,
+ PAGES = {673-688},
+ PDF = {huelsenbeck2002b.syst-biol.pdf},
+ DOI = {10.1080/10635150290102366},
+ PMID = {},
+ KEYWORDS = {Bayesian inference; Markov chain Monte Carlo; phylogeny; posterior probability}
+ }
+
+ at ARTICLE{huelsenbeck2004,
+ AUTHOR = {Huelsenbeck, John P. and Larget, Bret and Alfaro, Michael E.},
+ YEAR = 2004,
+ TITLE = {Bayesian Phylogenetic Model Selection Using Reversible Jump {Markov} Chain {Monte Carlo}},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 21,
+ PAGES = {1123-1133},
+ PDF = {huelsenbeck2004.mbe.pdf},
+ DOI = {10.1093/molbev/msh123},
+ PMID = {15034130},
+ KEYWORDS = {Bayesian phylogenetic inference; Markov chain Monte Carlo; maximum likelihood; reversible jump Markov chain Monte Carlo; substitution models}
+ }
+
+ at ARTICLE{hughes2000,
+ AUTHOR = {Hughes, Austin L. and Friedman, Robert},
+ YEAR = 2000,
+ TITLE = {Evolutionary Diversification of Protein-Coding Genes of Hantaviruses},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 17,
+ PAGES = {1558-1568},
+ PDF = {hughes2000.mbe.pdf},
+ DOI = {},
+ PMID = {11018161},
+ KEYWORDS = {adaptive evolution; Bunyaviridae; Hantavirus; host-parasite coevolution; viral evolution}
+ }
+
+ at ARTICLE{hughes2002,
+ AUTHOR = {Hughes, Austin L.},
+ YEAR = 2002,
+ TITLE = {Adaptive evolution after gene duplication},
+ JOURNAL = {Trends Genet.},
+ VOLUME = 18,
+ PAGES = {433-434 },
+ PDF = {hughes2002.tig.pdf},
+ DOI = {10.1016/S0168-9525(02)02755-5},
+ PMID = {},
+ KEYWORDS = {adaptive evolution; gene duplication; foregut fermentation; gene duplication; protein function; ribonuclease}
+ }
+
+ at ARTICLE{hughes2004,
+ AUTHOR = {Hughes, Timothy and Hyun, Young and Liberles, David A.},
+ YEAR = 2004,
+ TITLE = {Visualising very large phylogenetic trees in three dimensional hyperbolic space},
+ JOURNAL = {BMC Bioinformatics},
+ VOLUME = 5,
+ PAGES = {48},
+ PDF = {hughes2004.bmc-bioinformatics.pdf},
+ DOI = {doi:10.1186/1471-2105-5-48},
+ PMID = {},
+ SOURCE = {http://www.biomedcentral.com/1471-2105/5/48},
+ KEYWORDS = {Visualization; large phylogenetic trees; three dimensional hyperbolic space}
+ }
+
+ at ARTICLE{hughey1996,
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+ VOLUME = 12,
+ PAGES = {473-479},
+ PDF = {hughey1996.cabios.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing; sequence comparison; alignment; parallel hardware}
+ }
+
+ at ARTICLE{husmeier2001,
+ AUTHOR = {Husmeier, Dirk and Wright, Frank},
+ YEAR = 2001,
+ TITLE = {Probabilistic divergence measures for detecting interspecies recombination},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 17,
+ PAGES = {S123-S131},
+ PDF = {husmeier2001.bioinformatics.pdf},
+ DOI = {},
+ PMID = {11473001},
+ KEYWORDS = {recombination;; }
+ }
+
+ at ARTICLE{husmeier2002,
+ AUTHOR = {Husmeier, Dirk and Wright, Frank},
+ YEAR = 2002,
+ TITLE = {A {Bayesian} approach to discriminate between alternative {DNA} sequence segmentations},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 18,
+ PAGES = {226-234},
+ PDF = {husmeier2002.bioinformatics.pdf},
+ DOI = {},
+ PMID = {11847070},
+ KEYWORDS = {recombination;; rate variation; mosaic structure}
+ }
+
+ at ARTICLE{husmeier2002a,
+ AUTHOR = {Husmeier, Dirk and McGuire, Gr{\'a}inne},
+ YEAR = 2002,
+ TITLE = {Detecting recombination with MCMC},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 18,
+ PAGES = {345S-353S},
+ PDF = {husmeier2002a.bioinformatics.pdf},
+ DOI = {},
+ PMID = {12169565},
+ KEYWORDS = {recombination;; rate variation; mosaic structure}
+ }
+
+ at ARTICLE{husmeier2003,
+ AUTHOR = {Husmeier, Dirk and McGuire, Gr\�{a}inne},
+ YEAR = 2003,
+ TITLE = {Detecting Recombination in 4-Taxa {DNA} Sequence Alignments with {Bayesian Hidden Markov Models} and {Markov Chain Monte Carlo}},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 20,
+ PAGES = {315-337},
+ PDF = {husmeier2003.mbe.pdf},
+ DOI = {10.1093/molbev/msg039},
+ PMID = {12644553},
+ KEYWORDS = {phylogeny; DNA sequence alignment; recombination; hidden Markov models; Markov chain Monte Carlo}
+ }
+
+ at TECHREPORT{huson1997,
+ AUTHOR = {Huson, Daniel H.},
+ YEAR = 1997,
+ TITLE = {{SplitsTree}: A Program for Analyzing and Visualizing Evolutionary Data},
+ TYPE = {Materialien/Preprints},
+ NUMBER = 110,
+ INSTITUTION = {Universit\"at Bielefeld, Forschungsschwerpunkt Mathematisierung -- Stukturbildungsprozesse},
+ ADDRESS = {Bielefeld},
+ PDF = {hardcopy},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{huson1998,
+ AUTHOR = {Huson, Daniel H.},
+ YEAR = 1998,
+ TITLE = {{SplitsTree}: Analyzing and visualizing evolutionary data},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 14,
+ PAGES = {68-73},
+ PDF = {huson1998.bioinformatics.pdf},
+ DOI = {},
+ PMID = {9520503},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{huson1999,
+ AUTHOR = {Huson, D. H. and Nettles, S. M. and Warnow, T. J.},
+ YEAR = 1999,
+ TITLE = {Disk-Covering, a Fast-Converging Method for Phylogenetic Reconstruction},
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+ VOLUME = 6,
+ PAGES = {369-386},
+ PDF = {huson1999.jcb.pdf},
+ DOI = {10.1089/106652799318337},
+ PMID = {},
+ KEYWORDS = {algorithms; evolution; phylogenetic trees; clustering; Jukes Cantor; biomolecular data; chordal graphs}
+ }
+
+ at ARTICLE{huson2004,
+ AUTHOR = {Huson, Daniel H. and Steel, Mike},
+ YEAR = 2004,
+ TITLE = {Distances that Perfectly Mislead},
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+ PAGES = {327-332},
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+ DOI = {10.1080/10635150490423809},
+ PMID = {},
+ KEYWORDS = {Additive metric; distance-based phylogeny reconstruction; inconsistency}
+ }
+
+ at ARTICLE{huntley2000,
+ AUTHOR = {Huntley, Melanie and Golding, G. Brian},
+ YEAR = 2000,
+ TITLE = {Evolution of Simple Sequence in Proteins},
+ JOURNAL = {J. Mol. Evol.},
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+ PAGES = {131-140},
+ PDF = {huntley2000.jme.pdf},
+ DOI = {10.1007/s002390010073},
+ PMID = {10948269},
+ KEYWORDS = {Simple sequence; Low-complexity proteins; Amino acid repeats}
+ }
+
+ at ARTICLE{hurst2002,
+ AUTHOR = {Hurst, Laurence D.},
+ YEAR = 2002,
+ TITLE = {The {Ka/Ks} ratio: Diagnosing the form of sequence evolution},
+ JOURNAL = {Trends Genet.},
+ VOLUME = 18,
+ PAGES = {486-487},
+ PDF = {hurst2002.tig.pdf},
+ DOI = {10.1016/S0168-9525(02)02722-1},
+ PMID = {},
+ KEYWORDS = {nonsynomymous; synoymous; rate of evolution; neutral drift; natural selection}
+ }
+
+ at ARTICLE{hutter1998,
+ AUTHOR = {Hutter, Carolyn M. Hutter and Schug, Malcolm D. and Aquadro, Charles F.},
+ YEAR = 1998,
+ TITLE = {Microsatellite Variation in Drosophila melanogaster and Drosophila simulans: A Reciprocal Test of the Ascertainment Bias Hypothesis},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 15,
+ PAGES = {1620-1636},
+ PDF = {hutter1998.mbe.pdf},
+ DOI = {},
+ PMID = {9866198},
+ KEYWORDS = {Drosophila melanogaster; Drosophila simulans; microsatellite; simple sequence length polymorphism; ascertainment bias; dinucleotide repeat}
+ }
+
+ at ARTICLE{huynen1996,
+ AUTHOR = {Huynen, Martijn A.},
+ YEAR = 1996,
+ TITLE = {Exploring Phenotype Space Through Neutral Evolution},
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+ VOLUME = 43,
+ PAGES = {165-169},
+ PDF = {huynen1996.jme.pdf},
+ DOI = {},
+ PMID = {8703081},
+ KEYWORDS = {RNA secondary structure; neutral evolution; adaptive evolution; genotype-phenotype relation; sequence space; fitness landscape}
+ }
+
+ at ARTICLE{huynen1998,
+ AUTHOR = {Huynen, Martijn A. and van Nimwegen, Erik},
+ YEAR = 1998,
+ TITLE = {The Frequency Distribution of Gene Family Sizes in Complete Genomes},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 15,
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+ PDF = {huynen1998.mbe.pdf},
+ DOI = {},
+ PMID = {9580988},
+ KEYWORDS = {gene family; comparative genome analysis; powerlaw distribution}
+ }
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+ at ARTICLE{hyvoenen2004,
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+ TITLE = {Phylogeny of the {Polytrichales} ({Bryophyta}) based on simultaneous analysis of molecular and morphological data},
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+ PAGES = {915-928},
+ PDF = {hyvoenen2004.mpe.pdf},
+ DOI = {10.1016/j.ympev.2003.11.003},
+ PMID = {},
+ KEYWORDS = {combined analysis; simultaneous analysis; molecular data; morphological data}
+ }
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+
+ at ARTICLE{ibba2002,
+ AUTHOR = {Ibba, Michael},
+ YEAR = 2002,
+ TITLE = {{mRNA} decay: The big picture},
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+ PAGES = {335-336},
+ PDF = {ibba2002.tibs.pdf},
+ DOI = {10.1016/S0968-0004(02)02151-5},
+ PMID = {},
+ KEYWORDS = {MRNA decay; microarray}
+ }
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+ at ARTICLE{ina1998,
+ AUTHOR = {Ina, Yasuo},
+ YEAR = 1998,
+ TITLE = {Estimation of the Transition/Transversion Ratio},
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+ PAGES = {521-533},
+ PDF = {ina1998.jme.pdf},
+ DOI = {},
+ PMID = {9545463},
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+ }
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+ AUTHOR = {Inagaki, Yuji and Susko, Edward and Fast, Naomi M. and Roger, Andrew J.},
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+ TITLE = {Covarion Shifts Cause a Long-Branch Attraction Artifact That Unites {Microsporidia} and {Archaebacteria} in {EF-1$\alpha$} Phylogenies},
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+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 21,
+ PAGES = {1340-1349},
+ PDF = {inagaki2004.mbe.pdf},
+ REMARKS = {inagaki2004.mbe-supplement1.pdf},
+ DOI = {10.1093/molbev/msh130},
+ PMID = {15034136},
+ KEYWORDS = {phylogenetic artifact; long-branch attraction; EF-1alpha; microsporidia; covarion model; parallel site rate variation}
+ }
+
+ at ARTICLE{inoue2001,
+ AUTHOR = {Inoue, Jun G. and Miya, Masaki and Tsukamoto, Katsumi and Nishida, Mutsumi},
+ YEAR = 2001,
+ TITLE = {Complete Mitochondrial {DNA} Sequence of Conger myriaster (Teleostei: Anguilliformes): Novel Gene Order for Vertebrate Mitochondrial Genomes and the Phylogenetic Implications for Anguilliform Families},
+ JOURNAL = {J. Mol. Evol.},
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+ PAGES = {311-320},
+ PDF = {inoue2001.jme.pdf},
+ DOI = {10.1007/s002390010161},
+ PMID = {11343127},
+ KEYWORDS = {Gene rearrangement; Long PCR; Complete mtDNA sequence; Phylogenetic implications; Anguilliformes; Congroidei; Eels}
+ }
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+ at ARTICLE{iseli2002,
+ AUTHOR = {Iseli, Christian and Stevenson, Brian J. and de Souza, Sandro J. and Samaia, Helena B. and Camargo, Anamaria A. and Buetow, Kenneth H. and Strausberg, Robert L. and Simpson, Andrew J.G. and Bucher, Philipp and Jongeneel, C. Victor},
+ YEAR = 2002,
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+ at ARTICLE{iubmb1985,
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+ NOTE = {devised by the Nomenclature Committee of the International Union of Biochemistry (NC-IUB)}
+ }
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+ at ARTICLE{iupac1970,
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+ NOTE = {devised by the International Union of Pure and Applied Chemistry (IUPAC) and International Union of Biochemistry and Molecular Biology (IUB), IUPAC-IUB Commission on Biochemical Nomenclature (CBN)}
+ }
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+ at ARTICLE{iupac1984,
+ AUTHOR = {IUPAC-IUB},
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+ NOTE = {devised by the International Union of Pure and Applied Chemistry (IUPAC) and International Union of Biochemistry and Molecular Biology (IUB), IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)}
+ }
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+ at ARTICLE{iwabe1989,
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+ }
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+ at ARTICLE{jermiin1997,
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+ at ARTICLE{jiang1998,
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+ ADDRESS = {M{\"u}chen, Germany},
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+ PMID = {11796033},
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+ PMID = {},
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+
+ at ARTICLE{kendall1949,
+ AUTHOR = {Kendall, David G.},
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+ PDF = {kendall1949.j-r-stat-soc-b.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Stochastic Processes; Population Growth; Life-and-Death process; parameter estimation}
+ }
+
+ at ARTICLE{kent2002,
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+ YEAR = 2002,
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+ PAGES = {656-664},
+ PDF = {kent2002.genome-res.pdf},
+ DOI = {10.1101/gr.229202},
+ PMID = {11932250},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{kennedy2002,
+ AUTHOR = {Kennedy, M. and Page, R. D. M.},
+ YEAR = 2002,
+ TITLE = {Seabird supertrees: Combining partial estimates of procellariiform phylogeny},
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+ VOLUME = 119,
+ PAGES = {88-108},
+ KEYWORDS = {B gene-sequences, cytochrome-b, evolution, trees, shearwaters, petrels, pelecaniformes, information, parsimony, consensus, supertree},
+ PDF = {kennedy2002.auk.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
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+ PMID = {-},
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+ at ARTICLE{killian2001,
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+ at ARTICLE{kim1998,
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+
+ at INPROCEEDINGS{kim2001,
+ AUTHOR = {Kim, Junhyong and Salisbury, Benjamin A.},
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+ ADDRESS = {Hawaii},
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+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {Horizontal Gene Transfer; Median Tree Method; Supertree; Species Phylogeny}
+ }
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+ at ARTICLE{kimura1980,
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+ AUTHOR = {Kirchoff, B. K. and Richter, S. J. and Remington, D. L. and Wisniewski, E.},
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+
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+ AUTHOR = {Kishino, Hirohisa and Hasegawa, Masami},
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+ AUTHOR = {Kishino, Hirohisa and Miyata, Takashi and Hasegawa, Masami},
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+ at ARTICLE{kishino2001,
+ AUTHOR = {Kishino, Hirohisa and Thorne, Jeffrey L. and Bruno, William J.},
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+ at ARTICLE{kitano1999,
+ AUTHOR = {Kitano, Takashi and Saitou, Naruya},
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+ PDF = {kitano1999.jme.pdf},
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+ PMID = {10552043},
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+ }
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+ at ARTICLE{kjer2001,
+ AUTHOR = {Kjer, Karl M. and Blahnik, Roger J. and Holzenthal, Ralph W.},
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+ TITLE = {Phylogeny of Trichoptera (Caddisflies): Characterization of Signal and Noise Within Multiple Datasets},
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+ VOLUME = 50,
+ PAGES = {781-816},
+ PDF = {kjer2001.syst-biol.pdf},
+ DOI = {},
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+ KEYWORDS = {Annulipalpia; Bayesian inference; dataset combination; homoplasy; Integripalpia; Spicipalpia; pseudoreplicate reweighting}
+ }
+
+ at BOOK{klaeren1991,
+ AUTHOR = {Klaeren, Herbert},
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+ DOI = {},
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+ }
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+ at ARTICLE{kleinjung2002,
+ AUTHOR = {Kleinjung, Jens and Douglas, Nigel and Heringa, Jaap},
+ YEAR = 2002,
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+ DOI = {},
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+ KEYWORDS = {parallel bioinformatics; parallel computing}
+ }
+
+ at ARTICLE{klempa2003,
+ AUTHOR = {Klempa, Boris and Schmidt, Heiko A. and Ulrich, Rainer and Kaluz, Stefan and Labuda, Milan and Meisel, Helga and Hjelle, Brian and Kr\"uger, Detlev H.},
+ YEAR = 2003,
+ TITLE = {Genetic Interaction between Distinct {Dobrava Hantavirus} Subtypes in {Apodemus agrarius} and {A. flavicollis} in Nature},
+ JOURNAL = {J. Virol.},
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+ PAGES = {804-809},
+ PDF = {klempa2003.j-virol.pdf},
+ DOI = {10.1128/JVI.77.1.804-809.2003},
+ PMID = {12477889},
+ KEYWORDS = {Dobrava Virus; Hantavirus; Apodemus; Reassortment; Recombination}
+ }
+
+ at ARTICLE{klempa2003a,
+ AUTHOR = {Klempa, Boris and Ulrich, Rainer and Meisel, Helga and Kr\"uger, Detlev H. and Schmidt, Heiko A. and Kaluz, Stefan and Labuda, Milan and Hjelle, Brian},
+ YEAR = 2003,
+ TITLE = {Letter to the Editor: Genetic Interaction between {Dobrava} and {Saaremaa Hantaviruses}: Now or Millions of Years Ago? (Authors' Reply)},
+ JOURNAL = {J. Virol.},
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+ PAGES = {7157-7158},
+ PDF = {klempa2003a.j-virol.pdf},
+ DOI = {10.1128/JVI.77.12.7156-7158.2003},
+ PMID = {},
+ KEYWORDS = {hantavirus; recombination; interaction; reassortment}
+ }
+
+ at PHDTHESIS{klempa2004,
+ AUTHOR = {Klempa, Boris},
+ YEAR = 2004,
+ TITLE = {{Dobrava} and {Tula} hantaviruses from Central Europe: molecular evolution and pathogenic relevance},
+ SCHOOL = {Charit{\'e} School of Medicine, Humboldt University},
+ ADDRESS = {Berlin, Germany},
+ PDF = {klempa2004.phdthesis-prelim-3-3.pdf},
+ DOI = {},
+ PMID = {-},
+ KEYWORDS = {Hantavirus; Dobravavirus; DOBV; Tulavirus}
+ }
+
+ at MASTERSTHESIS{klingner2001,
+ AUTHOR = {Klingner, Jeff},
+ YEAR = 2001,
+ TITLE = {Visualizing Sets of Evolutionary Trees},
+ SCHOOL = {Department of Computer Science, University of Texas at Austin},
+ TYPE = {Undergraduate Thesis},
+ ADRESS = {USA},
+ PDF = {klingner2001.thesis.pdf},
+ MONTH = {May},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {Visualization technique; sets of Evolutionary trees; equally parsimonious trees; multidimensional scaling; Robinson-Foulds inter-tree distances; Mesquite}
+ }
+
+ at ARTICLE{klotz2003,
+ AUTHOR = {Klotz, Martin G. and Loewen, Peter C.},
+ YEAR = 2003,
+ TITLE = {The Molecular Evolution of Catalatic Hydroperoxidases: Evidence for Multiple Lateral Transfer of Genes Between Prokaryota and from Bacteria into Eukaryota},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 20,
+ PAGES = {1098-1112},
+ PDF = {klotz2003.mbe.pdf},
+ DOI = {10.1093/molbev/msg129},
+ PMID = {12777528},
+ KEYWORDS = {catalase; catalase-peroxidase; nonheme catalase; lateral gene transfer}
+ }
+
+ at ARTICLE{kluge1993,
+ AUTHOR = {Kluge, Arnold G. and Kolf, A. J.},
+ YEAR = 1993,
+ TITLE = {Cladistics: What's in a word?},
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+ PAGES = {183-199},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {??? Total Evidence; Cladistics; Consensus; Taxonomic Congruence}
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+ at ARTICLE{kluge1998,
+ AUTHOR = {Kluge, Arnold G.},
+ YEAR = 1998,
+ TITLE = {Total Evidence Or Taxonomic Congruence: Cladistics Or Consensus Classification},
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+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Total Evidence; Cladistics; Consensus; Taxonomic Congruence}
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+
+ at ARTICLE{kluge1999,
+ AUTHOR = {Kluge, Arnold G.},
+ YEAR = 1999,
+ TITLE = {The Science of Phylogenetic Systematics: Explanation, Prediction, and Test},
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+ at ARTICLE{knight2001,
+ AUTHOR = {Knight, Robin D. and Landweber, Laura F. and Yarus, Michael},
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+ TITLE = {How Mitochondria Redefine the Code},
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+ KEYWORDS = {Genetic code; Reassignment; Genome; Mutation}
+ }
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+ AUTHOR = {Knippers, Rolf and Philippsen, Peter and Sch{\"a}fer, Klaus P. and Fanning, Ellen},
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+ at ARTICLE{knoll1992,
+ AUTHOR = {Knoll, Andrew H.},
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+ at BOOK{knuth1997,
+ AUTHOR = {Knuth, Donald E.},
+ YEAR = 1997,
+ TITLE = {Fundamental Algorithms},
+ SERIES = {The Art of Computer Programming},
+ VOLUME = {1},
+ EDITION = {3},
+ PUBLISHER = {Addison-Wesley},
+ ADDRESS = {Reading, Massachusetts},
+ ISBN = {0-201-89683-4},
+ KEYWORDS = {}
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+ at BOOK{knuth1997a,
+ AUTHOR = {Knuth, Donald E.},
+ YEAR = 1997,
+ TITLE = {Seminumerical Algorithms},
+ SERIES = {The Art of Computer Programming},
+ VOLUME = {2},
+ EDITION = {3},
+ PUBLISHER = {Addison-Wesley},
+ ADDRESS = {Reading, Massachusetts},
+ ISBN = {0-201-89683-4},
+ KEYWORDS = {}
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+
+ at BOOK{knuth1997b,
+ AUTHOR = {Knuth, Donald E.},
+ YEAR = 1997,
+ TITLE = {Sorting and Searching},
+ SERIES = {The Art of Computer Programming},
+ VOLUME = {3},
+ EDITION = {3},
+ PUBLISHER = {Addison-Wesley},
+ ADDRESS = {Reading, Massachusetts},
+ ISBN = {0-201-89683-4},
+ KEYWORDS = {}
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+
+ at ARTICLE{kochut2003,
+ AUTHOR = {Kochut, Krys and Arnold, Jonathan and Sheth, Amit and Miller, John and Kraemer, Eileen and Arpinar, Budak and Cardoso, Jorge},
+ YEAR = 2003,
+ TITLE = {{IntelliGEN}: A Distributed Workflow System for Discovering Protein-Protein Interactions},
+ JOURNAL = {Distributed and Parallel Databases},
+ VOLUME = 13,
+ PAGES = {43-72},
+ PDF = {kochut2003.dpdb.pdf},
+ DOI = {10.1023/A:1021565722755},
+ PMID = {},
+ KEYWORDS = {parallel computing; parallel bioinformatics; parallel databases;; workflow management; biological process; bioinformatics; protein-protein interaction; laboratory information management}
+ }
+
+ at ARTICLE{koga1998,
+ AUTHOR = {Koga, Y. Kyuragi, T. and Nishihara, M. and Sone, N.},
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+ TITLE = {Did Archaeal and Bacterial Cells Arise Independently from Noncellular Precursors? A Hypothesis Stating That the Advent of Membrane Phospholipid with Enantiomeric Glycerophosphate Backbones Caused the Separation of the Two Lines of Descent},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 46,
+ PAGES = {54-63},
+ PDF = {koga1998.jme.pdf},
+ DOI = {},
+ PMID = {9419225},
+ KEYWORDS = {n-Glycerol-1-phosphate dehydrogenase; sn-Glycerol-3-phosphate dehydrogenase; Archaea; Bacteria; Ether-linked lipid; Differentiation; Cloning; Primary structure; egsA}
+ }
+
+ at ARTICLE{koga1998a,
+ AUTHOR = {Koga, Y. Kyuragi, T. and Nishihara, M. and Sone, N.},
+ YEAR = 1998,
+ TITLE = {Erratum: Did Archaeal and Bacterial Cells Arise Independently from Noncellular Precursors? A Hypothesis Stating That the Advent of Membrane Phospholipid with Enantiomeric Glycerophosphate Backbones Caused the Separation of the Two Lines of Descent},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 47,
+ PAGES = {631},
+ PDF = {koga1998a.jme-erratum.pdf},
+ DOI = {},
+ PMID = {9797414},
+ KEYWORDS = {n-Glycerol-1-phosphate dehydrogenase; sn-Glycerol-3-phosphate dehydrogenase; Archaea; Bacteria; Ether-linked lipid; Differentiation; Cloning; Primary structure; egsA}
+ }
+
+ at ARTICLE{kohne1970,
+ AUTHOR = {Kohne, D. E.},
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+ TITLE = {Evolution of higher--organism {DNA}},
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+ at ARTICLE{kokko1999,
+ AUTHOR = {Kokko, Hanna and Sutherland, William J.},
+ YEAR = 1999,
+ TITLE = {What do impact factors tell us? },
+ JOURNAL = {TREE},
+ VOLUME = 14,
+ PAGES = {382-384},
+ PDF = {kokko1999.tree.pdf},
+ DOI = {10.1016/S0169-5347(99)01711-5},
+ PMID = {},
+ KEYWORDS = {Impact factor; Citation index; Impact time window; Journal half-life; Research assessment exercise}
+ }
+
+ at INCOLLECTION{konagaya2002,
+ AUTHOR = {Konagaya, Akihiko},
+ TITLE = {{OBIGrid}: Towards a New Distributed Platform for Bioinformatics},
+ YEAR = 2002,
+ PAGES = {1-2},
+ BOOKTITLE = {Proceedings of the 21st IEEE Symposium on Reliable Distributed Systems (SRDS 02)},
+ PUBLISHER = {Computer Society},
+ ADDRESS = {},
+ PDF = {konagaya2002.SRDS2002.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing;; OBIGrid; Distributed Platform; Bioinformatics}
+ }
+
+ at ARTICLE{kondrashov1999,
+ AUTHOR = {Kondrashov, Alexey S.},
+ YEAR = 1999,
+ TITLE = {Comparative genomics and evolutionary biology},
+ JOURNAL = {Curr. Opin. Genet. Dev.},
+ VOLUME = 9,
+ PAGES = {624-629},
+ PDF = {kondrashov1999.curr-opin-genet-dev.pdf},
+ DOI = {10.1016/S0959-437X(99)00027-1},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at INPROCEEDINGS{konishi2002,
+ AUTHOR = {Konishi, Fumikazu and Fukuzaki, Akinobu and Satou, Kenji and Yamamoto, Tomoyuki and Defago, Xavier and Konagaya, Akihiko},
+ YEAR = 2002,
+ TITLE = {{OBIGrid}: A New Computing Platform for Bioinformatics},
+ BOOKTITLE = {Proceedings of the Genome Informatics Workshop XIII},
+ PAGES = {484-485},
+ SERIES = {Genome Informatics},
+ VOLUME = {13},
+ MONTH = {December},
+ PUBLISHER = {Universal Academy Press},
+ PDF = {konishi2002.GIW2002.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing;; grid computing, virtual private network; VPN; OBIGrid}
+ }
+
+ at ARTICLE{korall2004,
+ AUTHOR = {Korall, Petra and Kenrick, Paul},
+ YEAR = 2004,
+ TITLE = {The phylogenetic history of {Selaginellaceae} based on {DNA} sequences from the plastid and nucleus: extreme substitution rates and rate heterogeneity},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 31,
+ PAGES = {852-864},
+ PDF = {korall2004.mpe.pdf},
+ DOI = {10.1016/j.ympev.2003.10.014},
+ PMID = {},
+ KEYWORDS = {Combined analysis; plastid genes; nuclear genes; Selaginellaceae; Phylogeny; 26S rDNA; rbcL; Maximum parsimony; Bayesian inference; Long branches; Rate heterogeneity; Substitution rate}
+ }
+
+ at ARTICLE{korbel2002,
+ AUTHOR = {Korbel, Jan O. and Snel, Berend and Huynen, Martijn A. and Bork, Peer},
+ YEAR = 2002,
+ TITLE = {{SHOT}: A web server for the construction of genome phylogenies},
+ JOURNAL = {Trends Genet.},
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+ at ARTICLE{lee2002,
+ AUTHOR = {Lee, Christopher and Grasso, Catherine and Sharlow, Mark F.},
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+ JOURNAL = {Bioinformatics},
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+ TITLE = {Evolutionary genetics of invasive species},
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+ }
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+ at ARTICLE{lee2003,
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+ at ARTICLE{lee2003a,
+ AUTHOR = {Lee, Christopher},
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+ DOI = {},
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+ at ARTICLE{lee2003b,
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+ KEYWORDS = {parallel computing}
+ }
+
+ at ARTICLE{li1998,
+ AUTHOR = {Li, Chia--Wei and Chen, Jun--Yuan and Hua, Tzu--En},
+ YEAR = 1998,
+ TITLE = {Precambrian Sponges with Cellular Structures},
+ JOURNAL = {Science},
+ VOLUME = 279,
+ PAGES = {879-882},
+ PDF = {li1998.science.pdf},
+ DOI = {},
+ PMID = {9452391},
+ KEYWORDS = {}
+ }
+
+ at BOOK{li1997,
+ AUTHOR = {Li, Wen-Hsiung},
+ YEAR = 1997,
+ TITLE = {Molecular Evolution},
+ PUBLISHER = {Sinauer Associates},
+ ADDRESS = {Sunderland, Massachusetts}
+ }
+
+ at ARTICLE{li1996,
+ AUTHOR = {Li, Wen-Hsiung and Gu, Xun},
+ YEAR = 1996,
+ TITLE = {Estimating Evolutionary Distances between {DNA} Sequences},
+ JOURNAL = {Methods Enzymol.},
+ VOLUME = 266,
+ PAGES = {449-459},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at BOOK{li1991,
+ AUTHOR = {Li, Wen-Hsiung and Graur, Dan},
+ YEAR = 1991,
+ TITLE = {Fundamentals of Molecular Evolution},
+ PUBLISHER = {Sinauer Associates},
+ ADDRESS = {Sunderland, Massachusetts}
+ }
+
+ at ARTICLE{li1990,
+ AUTHOR = {Li, Wen--Hsiung and Gouy, Manolo},
+ YEAR = 1990,
+ TITLE = {Statistical Tests of Molecular Phylogenies},
+ JOURNAL = {Methods Enzymol.},
+ VOLUME = 183,
+ PAGES = {645-659},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{li2003,
+ AUTHOR = {Li, Jia and Miller, Webb},
+ YEAR = 2003,
+ TITLE = {Significance of Interspecies Matches when Evolutionary Rate Varies},
+ JOURNAL = {J. Comput. Biol.},
+ VOLUME = 10,
+ PAGES = {537-554},
+ PDF = {li2003.jcb.pdf},
+ DOI = {10.1089/10665270360688174},
+ PMID = {},
+ KEYWORDS = {DNA sequence alignment; p-values of interspecies matches; evolutionary rate; hidden Markov model; human chromosome 22}
+ }
+
+ at ARTICLE{li2003a,
+ AUTHOR = {Li, Kuo-Bin},
+ YEAR = 2003,
+ TITLE = {{ClustalW-MPI}: {ClustalW} analysis using distributed and parallel computing},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 19,
+ PAGES = {1585-1586},
+ PDF = {li2003a.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg192},
+ PMID = {12912844},
+ KEYWORDS = {parallel bioinformatics; parallel computing; ClustalW; MPI; multiple sequence alignment}
+ }
+
+ at ARTICLE{liberles2001,
+ AUTHOR = {Liberles, David A.},
+ YEAR = 2001,
+ TITLE = {Evaluation of Methods for Determination of a Reconstructed History of Gene Sequence Evolution},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 18,
+ PAGES = {2040-2047},
+ PDF = {liberles2001.mbe.pdf},
+ DOI = {},
+ PMID = {11606700},
+ KEYWORDS = {nonsynonymous nucleotide substitution; synonymous nucleotide substitution; PAM distance; adaptive evolution; reconstructed ancestral sequences}
+ }
+
+ at PHDTHESIS{liebers2000,
+ AUTHOR = {Liebers, Dorit},
+ YEAR = 2000,
+ TITLE = {{Systematik} und {Taxonomie} der {Gro\ss{}m{\"o}ven} der \textit{{Larus}--argentus--cachinnans--fuscus} {Gruppe} in {Eurasien}. Phylogenetische Differenzierung anhand mitochondraler {D-Loop} Sequenzen},
+ SCHOOL = {Ernst--Moritz--Arndt--Universit\"at Greifswald},
+ ADDRESS = {Germany},
+ PDF = {NICHT VORHANDEN},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{liebers2001,
+ AUTHOR = {Liebers, D. and Helbig, A. J. and de Knijff, P.},
+ YEAR = 2001,
+ TITLE = {Genetic differentiation and phylogeography of gulls in the {Larus cachinnans} -- fuscus group ({Aves: Charadriiformes})},
+ JOURNAL = {Mol. Ecol.},
+ VOLUME = 10,
+ PAGES = {2447--2462},
+ PDF = {liebers2001.mol-ecol.pdf},
+ DOI = {10.1046/j.0962-1083.2001.01370.x},
+ PMID = {},
+ KEYWORDS = {Dorit; DFG}
+ }
+
+ at ARTICLE{liebers2002,
+ AUTHOR = {Liebers, D. and Helbig, A. J.},
+ YEAR = 2002,
+ TITLE = {Phylogeography and colonization history of {Lesser Black-backed Gulls} ({Larus fuscus}) as revealed by {mtDNA} sequences},
+ JOURNAL = {J. Evol. Biol.},
+ VOLUME = 15,
+ PAGES = {1021--1033},
+ PDF = {liebers2002.jeb.pdf},
+ DOI = {10.1046/j.1420-9101.2002.00454.x},
+ PMID = {},
+ KEYWORDS = {Dorit; DFG}
+ }
+
+ at INCOLLECTION{liebers2002a,
+ AUTHOR = {Liebers, Dorit and Schmidt, Heiko A. and Vingron, Martin and von Haeseler, Arndt},
+ TITLE = {Computer assisted phylogenetic analysis of large genomic datasets},
+ YEAR = 2002,
+ PAGES = {66-67},
+ EDITOR = {Wadzack, J{\"o}rg and Haese, Angela and L{\"o}hmer, Birgit},
+ BOOKTITLE = {Progress Report 1999 - 2002: German Human Genome Project},
+ PUBLISHER = {Druckhaus Schmergow},
+ ADDRESS = {Berlin, Germany},
+ PDF = {liebers2002a.DHGP2002.pdf},
+ DOI = {-},
+ PMID = {-},
+ ISBN = {3-00-010097-0},
+ KEYWORDS = {DHGP Progress Report}
+ }
+
+ at ARTICLE{liebers2003,
+ AUTHOR = {Liebers, D. and Meyer, S. and Helbig, A. J. and von Haeseler, A.},
+ YEAR = 2003,
+ TITLE = {Mutational hot spots in the mitochondrial hypervariable region I of gulls ({Aves: Laridae})},
+ JOURNAL = {J. Mol. Evol.},
+ MISSINGVOLUME = {},
+ PAGES = {submitted},
+ PDF = {NICHT VORHANDEN},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Dorit; DFG}
+ }
+
+ at ARTICLE{liebers2004,
+ AUTHOR = {Liebers, D. and de Knijff, P. and Helbig, A. J.},
+ YEAR = 2004,
+ TITLE = {The {Herring Gull} {Larus argentatus} is not a ring species},
+ JOURNAL = {Proc. R. Soc. Lond. B},
+ VOLUME = {271},
+ PAGES = {893-901},
+ PDF = {liebers2004.proc-rsoc-b.pdf},
+ DOI = {10.1098/rspb.2004.2679},
+ PMID = {},
+ KEYWORDS = {Dorit; DFG;; speciation; ring-species model; Larus argentatus complex; mitochondrial control region; cytochrome b gene; phylogeography}
+ }
+
+ at BOOK{libscomb1998,
+ AUTHOR = {Diana Lipscomb},
+ YEAR = 1998,
+ TITLE = {Cladistic Analysis Using Hennig86},
+ PUBLISHER = {George Washington University},
+ ADDRESS = {USA},
+ ISBN = {-},
+ PDF = {libscomb1998.hennig86.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{liden1999,
+ AUTHOR = {Lid{\'e}n, Magnus},
+ YEAR = 1999,
+ TITLE = {Boots-traps},
+ JOURNAL = {Taxon},
+ VOLUME = 48,
+ PAGES = {349-350},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {bootstrap; phylogenetic trees; weighted characters}
+ }
+
+ at BOOK{liebecq1992,
+ EDITOR = {Li\'{e}becq, C.},
+ YEAR = 1992,
+ TITLE = {Biochemical Nomenclature and Related Documents},
+ EDITION = 2,
+ PUBLISHER = {Portland Press},
+ ADDRESS = {London},
+ ISBN = {1-85578-005-4},
+ KEYWORDS = {Nomenclature, IUPAC codes, amino acids, nucleotides},
+ REMARKS = {IUPAC-IUBMB, http://www.chem.qmul.ac.uk/iupac/bibliog/white.html}
+ }
+
+ at INPROCEEDINGS{likhoded1999,
+ AUTHOR = {Likhoded, N. A.},
+ YEAR = 1999,
+ TITLE = {Two-Dimensional Scheduling of Algorithms with Uniform Dependencies},
+ BOOKTITLE = {Proceedings of the 5th International Conference on Parallel Computing Technologies (PaCT-99)},
+ SERIES = {Lecture Notes in Computer Science},
+ VOLUME = 1662,
+ PAGES = {92-97},
+ PUBLISHER = {Springer},
+ ADDRESS = {New York},
+ PDF = {likhoded1999.LNCS.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel computing; scheduling; affine scheduling}
+ }
+
+ at ARTICLE{lin2002,
+ AUTHOR = {Lin, Yu-Hsin and McLenachan, Patricia A. and Gore, Alicia R. and Phillips, Matthew J. and Ota, Rissa and Hendy, Michael D. and Penny, David},
+ YEAR = 2002,
+ TITLE = {Four New Mitochondrial Genomes and the Increased Stability of Evolutionary Trees of Mammals from Improved Taxon Sampling},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 19,
+ PAGES = {2060-2070},
+ PDF = {lin2002.mbe.pdf},
+ DOI = {},
+ PMID = {12446798},
+ KEYWORDS = {bats; insectivores; mammal evolution; mitochondrial genomes; taxon sampling; tree comparisons; triple Markov analysis}
+ }
+
+ at ARTICLE{lin2004,
+ AUTHOR = {Lin, Chung-Ping and Danforth, Bryan N.},
+ YEAR = 2004,
+ TITLE = {How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 30,
+ PAGES = {686-702},
+ PDF = {lin2004.mpe.pdf},
+ DOI = {10.1016/S1055-7903(03)00241-0},
+ PMID = {},
+ KEYWORDS = {Insect phylogeny; Molecular evolution; Bayesian analysis; combined analysis}
+ }
+
+ at ARTICLE{ling2002,
+ AUTHOR = {Ling, Lunjiang and Wang, Jinhua and Cui, Yan and Li, Wei and Chen, Runsheng},
+ YEAR = 2002,
+ TITLE = {Proteome-wide analysis of protein function composition reveals the clustering and phylogenetic properties of organisms},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 25,
+ PAGES = {101-111},
+ PDF = {ling2002.mpe.pdf},
+ DOI = {10.1016/S1055-7903(02)00354-8},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{lio1998,
+ AUTHOR = {Li\`{o}, Pietro and Goldman, Nick},
+ YEAR = 1998,
+ TITLE = {Models of Molecular Evolution and Phylogeny},
+ JOURNAL = {Genome Res.},
+ VOLUME = 8,
+ PAGES = {1233-1244},
+ PDF = {lio1998.genome-res.pdf},
+ DOI = {},
+ PMID = {9872979},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{lio2002,
+ AUTHOR = {Li\`{o}, Pietro and Goldman, Nick},
+ YEAR = 2002,
+ TITLE = {Modeling Mitochondrial Protein Evolution Using Structural Information},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 54,
+ PAGES = {519-529},
+ PDF = {lio2002.jme.pdf},
+ DOI = {10.1007/s00239001-0052-7},
+ PMID = {11956690},
+ KEYWORDS = {Hidden Markov models; Maximum likelihood; Mitochondria; Models of evolution; Phylogeny; Transmembrane proteins}
+ }
+
+ at MISC{lipscomb1998,
+ AUTHOR = {Lipscomb, Diana},
+ YEAR = 1998,
+ TITLE = {Basics of Cladistic Analysis},
+ HOWPUPLISHED = {http://www.gwu.edu/\%7Eclade/faculty/lipscomb/Cladistics.pdf},
+ PDF = {lipscomb1998.Cladistics.pdf}
+ }
+
+ at ARTICLE{lipscomb2003,
+ AUTHOR = {Lipscomb, Diana and Platnick, N. and Wheeler, Q.},
+ YEAR = 2003,
+ TITLE = {The intellectual content of taxonomy: a comment on {DNA} taxonomy},
+ JOURNAL = {TREE},
+ VOLUME = 18,
+ PAGES = {65-66},
+ PDF = {lipscomb2003.tree.pdf},
+ DOI = {10.1016/S0169-5347(02)00060-5},
+ PMID = {},
+ KEYWORDS = {DNA taxonomy; systematics}
+ }
+
+ at ARTICLE{liu2001,
+ AUTHOR = {Liu, F. G. and Miyamoto, M. M. and Freire, N. P. and Ong, P. Q. and Tennant, M. R. and Young, T. S. and Gugel, K. F.},
+ YEAR = 2001,
+ TITLE = {Molecular and morphological supertrees for eutherian (placental) mammals},
+ JOURNAL = {Science},
+ VOLUME = 291,
+ PAGES = {1786-1789},
+ PDF = {liu2001.science.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertree}
+ }
+
+ at INPROCEEDINGS{liu2001a,
+ AUTHOR = {Liu, Juan and Iba, Hitoshi and Ishizuka, Mitsuru},
+ YEAR = 2001,
+ TITLE = {Selecting Informative Genes with Parallel Genetic Algorithms in Tissue Classification},
+ BOOKTITLE = {Proceedings of the Genome Informatics Workshop XII},
+ PAGES = {14-23},
+ SERIES = {Genome Informatics},
+ VOLUME = {12},
+ MONTH = {December},
+ PUBLISHER = {Universal Academy Press},
+ PDF = {liu2001a.GIW2001.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing; tissue classification; gene expression level; gene selection; parallel genetic algorithm}
+ }
+
+ at ARTICLE{lobry1999,
+ AUTHOR = {Lobry, J. R. and Lobry, C.},
+ TITLE = {Evolution of {DNA} Base Composition Under No-Strand-Bias Conditons When the Substitution Rates Are Not Constant},
+ JOURNAL = {Mol. Biol. Evol.},
+ YEAR = 1999,
+ VOLUME = 16,
+ PAGES = {719-723},
+ PDF = {lobry1999.mbe.pdf},
+ DOI = {},
+ PMID = {10368950},
+ KEYWORDS = {molecular evolution; DNA base composition; GC content; parity rules; base composition skew; mathematical model}
+ }
+
+ at ARTICLE{lockhart1994,
+ AUTHOR = {Lockhart, P. J. and Steel, M. A. and Hendy, M. D. and Penny, D.},
+ YEAR = 1994,
+ TITLE = {Recovering evolutionary trees under a more realistic model of sequence evolution},
+ JOURNAL = {Mol. Biol. Evol.},
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+ PDF = {lockhart1994.mbe.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {amniotes; nucleotide composition; chloroplast origins; determinants; evolutionary models; evolutionary trees; honeybees}
+ }
+
+ at ARTICLE{lockhart2001,
+ AUTHOR = {Lockhart, Peter J. and McLenachan, Patricia A. and Havell, David and Glenny, David and Huson, Daniel and Jensen, Uwe},
+ YEAR = 2001,
+ TITLE = {Phylogeny, Radiation, and Transoceanic Dispersal of New Zealand Alpine Buttercups: Molecular Evidence under Split Decomposition},
+ JOURNAL = {Ann. Mo. Bot. Gard.},
+ VOLUME = 88,
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+ PDF = {hardcopy},
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+ KEYWORDS = {alpine radiation; dispersal; phylogeny; quartet puzzling; Ranunculus; split decomposition}
+ }
+
+ at BOOK{lodish1995,
+ AUTHOR = {Lodish, Harvey and Baltimore, David and Berk, Arnold and Zipursky, S. Lawrence and Matsudaira and Darnell, James},
+ YEAR = 1995,
+ TITLE = {Molecular Cell Biology},
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+ PUBLISHER = {Scientific American Books},
+ ADDRESS = {New York}
+ }
+
+ at ARTICLE{loeytynoja2003,
+ AUTHOR = {L{\"o}ytynoja, Ari and Milinkovitch, Michel C.},
+ YEAR = 2003,
+ TITLE = {A hidden Markov model for progressive multiple alignment},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 19,
+ PAGES = {1505-1513},
+ PDF = {loeytynoja2003.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg193},
+ PMID = {12912831},
+ KEYWORDS = {hidden Markov model; HMM; progressive multiple alignment}
+ }
+
+ at ARTICLE{lombard2002,
+ AUTHOR = {Lombard, V. and Camon, E. B. and Parkinson, H. E. Hingamp, P. and Stoesser, G. and Redaschi, N.},
+ YEAR = 2002,
+ TITLE = {{EMBL-Align}: A new public nucleotide and amino acid multiple sequence alignment database},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 18,
+ PAGES = {763-764},
+ PDF = {lombard2002.bioinformatics.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{long2003,
+ AUTHOR = {Long, Manyuan and Betr{\'a}n, Esther and Thornton, Kevin and Wang, Wen},
+ YEAR = 2003,
+ TITLE = {The Origin of New Genes: Glimpses from the Young and Old},
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+ PDF = {long2003.net-rev-genet.pdf},
+ DOI = {10.1038/nrg1204},
+ PMID = {},
+ KEYWORDS = {Origin of New Genes}
+ }
+
+ at ARTICLE{lopez1999,
+ AUTHOR = {Lopez, Philippe and Forterre, Patrick and Philippe, Herv{\'e}},
+ YEAR = 1999,
+ TITLE = {The Root of the Tree of Life in the Light of the Covarion Model},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 49,
+ PAGES = {496-508},
+ PDF = {lopez1999.jme.pdf},
+ DOI = {},
+ PMID = {10486007},
+ KEYWORDS = {Covarion; Root of the tree of life; Elongation factors; Mutational saturation; Long branch attraction}
+ }
+
+ at ARTICLE{lopez2002,
+ AUTHOR = {Lopez, P. and Casane, D. and Philippe, H.},
+ YEAR = 2002,
+ TITLE = {Heterotachy, an Important Process of Protein Evolution},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 19,
+ PAGES = {1-7},
+ PDF = {lopez2002.mbe.pdf},
+ DOI = {},
+ PMID = {11752184},
+ KEYWORDS = {covarion; cytochrome b; molecular evolution; phylogeny; vertebrates}
+ }
+
+ at ARTICLE{losos2003,
+ AUTHOR = {Losos, Jonathan B. and Glor, Richard E.},
+ YEAR = 2003,
+ TITLE = {Phylogenetic comparative methods and the geography of speciation},
+ JOURNAL = {TREE},
+ VOLUME = 18,
+ PAGES = {220-227},
+ PDF = {losos2003.tree.pdf},
+ DOI = {10.1016/S0169-5347(03)00037-5},
+ PMID = {},
+ KEYWORDS = {Phylogenetic comparative methods; geography of speciation}
+ }
+
+ at ARTICLE{louie2003,
+ AUTHOR = {Louie, Elizabeth and Ott, Jurg and Majewski, Jacek},
+ YEAR = 2003,
+ TITLE = {Nucleotide Frequency Variation Across Human Genes},
+ JOURNAL = {Genome Res.},
+ VOLUME = 13,
+ PAGES = {2594-2601},
+ PDF = {louie2003.genome-res.pdf},
+ DOI = {10.1101/gr.1317703},
+ PMID = {14613976},
+ KEYWORDS = {Nucleotide Frequency; Human Genes}
+ }
+
+ at ARTICLE{lumbsch2004,
+ AUTHOR = {Lumbsch, H. Thorsten and Schmitt, Imke and Palice, Zdenek and Wiklund, Elisabeth and Ekman, Stefan and Wedin, Mats},
+ YEAR = 2004,
+ TITLE = {Supraordinal phylogenetic relationships of {Lecanoromycetes} based on a {Bayesian} analysis of combined nuclear and mitochondrial sequences},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 31,
+ PAGES = {822-832},
+ PDF = {lumbsch2004.mpe.pdf},
+ DOI = {10.1016/j.ympev.2003.11.001},
+ PMID = {},
+ KEYWORDS = {Bayesian analysis; combined analysis; nuclear genes; mitochondrial genes; nuclear sequences; mitochondrial sequences}
+ }
+
+ at ARTICLE{lundin1999,
+ AUTHOR = {Lundin, Lars-G.},
+ YEAR = 1999,
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+ VOLUME = 10,
+ PAGES = {523-530},
+ PDF = {lundin1999.scdb.pdf},
+ DOI = {10.1006/scdb.1999.0333},
+ PMID = {},
+ KEYWORDS = {multicellularity; bilateria; diploblasts; triploblasts; metazoa; Cambrian explosion; gene-genome duplication}
+ }
+
+ at ARTICLE{lundkvist1997,
+ AUTHOR = {Lundkvist, {\AA}ke and Vasilenko, Vera and Golovljova, Irina and Plyusnin, Alexander and Vaheri, Antti},
+ YEAR = 1997,
+ TITLE = {{Dobrava} hantavirus outbreak in {Russia}},
+ JOURNAL = {Lancet},
+ VOLUME = 350,
+ PAGES = {781-782},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {9298001},
+ KEYWORDS = {Dobrava hantavirus; Russia}
+ }
+
+ at ARTICLE{lundkvist1998,
+ AUTHOR = {Lundkvist, {\AA}ke and Vasilenko, Vera and Golovljova, Irina and Plyusnin, Alexander and Vaheri, Antti},
+ YEAR = 1997,
+ TITLE = {Human {Dobrava} hantavirus infections in {Estonia}},
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+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Dobrava hantavirus; Estonia}
+ }
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+ at ARTICLE{lunter2003,
+ AUTHOR = {Lunter, G. A. and Mikl{\'o}s, I. and Song, Y. S. and Hein, J.},
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+ PDF = {lunter2003.jcb.pdf},
+ DOI = {10.1089/106652703322756122},
+ PMID = {},
+ KEYWORDS = {statistical alignment; multiple alignment; phylogeny; maximum likelihood}
+ }
+
+ at ARTICLE{luo2001,
+ AUTHOR = {Luo, Zhe-Xi and Cifelli, Richard L. and Kielan-Jaworowska, Zofia},
+ YEAR = 2001,
+ TITLE = {Dual origin of tribosphenic mammals},
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+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
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+ at ARTICLE{luo2002,
+ AUTHOR = {Luo, Zhe-Xi and Kielan-Jaworowska, Zofia and Cifelli, Richard L.},
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+ PMID = {},
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+ }
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+ AUTHOR = {Lutzoni, Francois and Barker, F. Keith},
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+ DOI = {},
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+ }
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+ }
+
+ at INPROCEEDINGS{matsuda1993a,
+ AUTHOR = {Matsuda, Hideo},
+ YEAR = 1993,
+ TITLE = {Efficient Query Processing on Genomic Database using Data-Parallel Logic Programming Language},
+ BOOKTITLE = {Proceedings of the Genome Informatics Workshop IV},
+ PAGES = {17-24},
+ MONTH = {December},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ REMARKS = {
+% http://ieeexplore.ieee.org/xpl/abs_free.jsp?isNumber=9154&prod=CNF&arnumber=407169&arSt=280&ared=283+vol.1&arAuthor=Matsuda%2C+H.%3B+Olsen%2C+G.J.%3B+Hagstrom%2C+R.%3B+Overbeek%2C+R.%3B+Kaneda%2C+Y.&arNumber=407169&a_id0=407166&a_id1=407167&a_id2=407168&a_id3=407169&a_id4=407170&a_id5=407171&a_id6=407172&a_id7=407173&a_id8=407174&a_id9=407175&a_id10=407176&a_id11=407177&a_id12=407178&a_id13=407179&a_id14=407180&count=15
+},
+ KEYWORDS = {parallel bioinformatics; parallel computing; Genomic Database; Data-Parallel; Logic Programming Language}
+ }
+
+ at UNPUBLISHED{matsuda1994,
+ AUTHOR = {Matsuda, Hideo and Hagstrom, Ray and Overbeek, Ross and Kaneda, Yukio},
+ YEAR = 1994,
+ TITLE = {Implementation of a parallel processing system for inference of phylogenetic trees},
+ NOTE = {unpublished},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing; phylogeny}
+}
+
+ at INPROCEEDINGS{matsuda1994a,
+ AUTHOR = {Matsuda, Hideo and Olsen, Gary J. and Overbeek, Ross and Kaneda, Yukio},
+ YEAR = 1994,
+ TITLE = {Fast Phylogenetic Analysis on a Massively Parallel Machine},
+ BOOKTITLE = {Proceedings of the 8th ACM International Conference on Supercomputing},
+ PAGES = {297-302},
+ MONTH = {July},
+ PDF = {matsuda1994a.ICS.pdf},
+ DOI = {},
+ PMID = {10.1145/181181.181545},
+ KEYWORDS = {parallel bioinformatics; parallel computing; phylogeny}
+ }
+
+ at ARTICLE{matsuda1994b,
+ AUTHOR = {Matsuda, Hideo and Kaneda, Yukio},
+ YEAR = 1994,
+ TITLE = {An Application of an {OR}-Parallel {Prolog} System to Phylogenetic Analysis},
+ JOURNAL = {Lisp Symb. Comput.},
+ VOLUME = {7},
+ PAGES = {211-229},
+ PDF = {NICHT VORHANDEN},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; Artificial intelligence; Bacteriology; C (programming language); Calculations; Logic programming; Mathematical models; Maximum likelihood method; Optimization; or parallelism; Parallel algorithms; Phylogenetic analysis; Priority mechanism; prolog (programming language); Search algorithm; Statistical methods; Symbolic computing; Trees (mathematics)},
+}
+
+ at INPROCEEDINGS{matsuda1994c,
+ AUTHOR = {Matsuda, Hideo and Yamashita, Hiroshi and Kaneda, Yukio},
+ YEAR = 1994,
+ TITLE = {Molecular Phylogenetic Analysis using both {DNA} and Amino Acid Sequence Data and Its Parallelization},
+ BOOKTITLE = {Proceedings of the Genome Informatics Workshop V},
+ PAGES = {120-129},
+ MONTH = {December},
+ PUBLISHER = {Universal Academy Press},
+ PDF = {matsuda1994c.GIW1994.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing; phylogeny}
+ }
+
+ at INPROCEEDINGS{matsuda1995,
+ AUTHOR = {Matsuda, Hideo},
+ YEAR = 1995,
+ TITLE = {Construction of Phylogenetic Trees from Amino Acid Sequences using a Genetic Algorithm},
+ BOOKTITLE = {Proceedings of the Genome Informatics Workshop VI},
+ PAGES = {19-28},
+ MONTH = {December},
+ PUBLISHER = {Universal Academy Press},
+ PDF = {matsuda1995.GIW1995.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {phylogeny; tree; GA; genetic algorithm}
+ }
+
+ at INPROCEEDINGS{matsuda1995a,
+ AUTHOR = {Matsuda, Hideo},
+ YEAR = 1995,
+ TITLE = {Querying Genomic Database by using a Parallel Logic Programming System on Distributed Computing Environment},
+ BOOKTITLE = {Proceedings of the IEEE Pacific Rim Conference on Communications, Computers, and Signal Processing},
+ PAGES = {333-336},
+ MONTH = {May},
+ PDF = {NICHT VORHANDEN},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing; Genomic Database; Data-Parallel; Logic Programming Language; Distributed Computing Environment}
+ }
+
+ at INPROCEEDINGS{matsuda1996,
+ AUTHOR = {Matsuda, Hideo},
+ YEAR = 1996,
+ TITLE = {Protein Phylogenetic Inference using Maximum Likelihood With A Genetic Algorithm},
+ BOOKTITLE = {Proceedings of the 1st Pacific Symposium on Biocomputing (PSB 1996)},
+ PAGES = {512-523},
+ MONTH = {January},
+ ADDRESS = {Hawaii},
+ PDF = {matsuda1996.PSB1996.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing; phylogeny}
+ }
+
+ at INPROCEEDINGS{matsumoto2000,
+ AUTHOR = {Matsumoto, Toshiko and Sadakane, Kunihiko and Imai, Hiroshi},
+ YEAR = 2000,
+ TITLE = {Biological Sequence Compression Algorithms},
+ BOOKTITLE = {Proceedings of the Genome Informatics Workshop X},
+ PAGES = {43-52},
+ SERIES = {Genome Informatics},
+ VOLUME = {10},
+ MONTH = {December},
+ PUBLISHER = {Universal Academy Press},
+ PDF = {matsumoto2000.GIW2000.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {DNA,protein,compression,context tree weighting}
+ }
+
+ at ARTICLE{matsuoka2002,
+ AUTHOR = {Matsuoka, Yoshihiro and Vigouroux, Yves and Goodman, Major M. and Sanchez G., Jesus and Buckler, Edward and Doebley, John},
+ YEAR = 2002,
+ TITLE = {A single domestication for maize shown by multilocus microsatellite genotyping},
+ JOURNAL = {Proc. Natl. Acad. Sci. USA},
+ VOLUME = 99,
+ PAGES = {6080-6084},
+ PDF = {matsuoka2002.pnas.pdf},
+ DOI = {10.1073/pnas.052125199},
+ PMID = {11983901},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{matte2002,
+ AUTHOR = {Matte-Tailliez, Oriane and Brochier, C\'{e}line and Forterre, Patrick and Philippe, Herv\'{e}},
+ YEAR = 2002,
+ TITLE = {Archaeal Phylogeny Based on Ribosomal Proteins},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 19,
+ PAGES = {631-639},
+ PDF = {matte2002.mbe.pdf},
+ DOI = {},
+ PMID = {11961097},
+ KEYWORDS = {Archaea; lateral gene transfer; molecular phylogeny; multigene analysis; ribosomal proteins}
+ }
+
+ at ARTICLE{mattern2004,
+ AUTHOR = {Mattern, Michelle Y.},
+ YEAR = 2004,
+ TITLE = {Molecular phylogeny of the Gasterosteidae: the importance of using multiple genes},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 30,
+ PAGES = {366-377},
+ PDF = {mattern2004.mpe.pdf},
+ DOI = {10.1016/S1055-7903(03)00190-8},
+ PMID = {},
+ KEYWORDS = {combined analyses;; 12S rRNA; 16S rRNA; Apeltes; ATPase 6; Control region; Culaea; Cytochrome b; Gasterosteidae; Gasterosteus; Mitochondrial DNA; Molecular; Phylogeny; Pungitius; Spinachia; Stickleback}
+ }
+
+ at ARTICLE{maxam1977,
+ AUTHOR = {Maxam, A. M. and Gilbert, W.},
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+ TITLE = {A New Method for Sequencing {DNA}},
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+ VOLUME = 74,
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+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {DNA sequencing}
+ }
+
+ at ARTICLE{mayer2000,
+ AUTHOR = {Mayer, Klaus F. X. and Lemcke Kai and Sch{\"u}ller Christine M. and Rudd Stephen and Zaccaria Paolo},
+ YEAR = 2000,
+ TITLE = {Arabidopsis genome analysis as exemplified by analysis of chromosome 4},
+ JOURNAL = {Brief. Bioinform.},
+ VOLUME = 1,
+ PAGES = {389-397},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
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+ at ARTICLE{maynardsmith1992,
+ AUTHOR = {Maynard~Smith, J.},
+ YEAR = 1992,
+ TITLE = {Analyzing the mosaic structure of genes},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 34,
+ PAGES = {126-129},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {1556748},
+ KEYWORDS = {Mosaic structure; recombination; genetic information; Penicillin resistance}
+ }
+
+ at ARTICLE{maynardsmith1998,
+ AUTHOR = {Maynard~Smith, J. and Smith, N. H.},
+ YEAR = 1998,
+ TITLE = {Detecting Recombination from Gene Trees},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 15,
+ PAGES = {590-599},
+ PDF = {maynardsmith1998.mbe.pdf},
+ DOI = {},
+ PMID = {9580989},
+ KEYWORDS = {homoplasy test; effective number of sites; recombination; gene trees}
+ }
+
+ at ARTICLE{maynardsmith2002,
+ AUTHOR = {Maynard~Smith, J. and Smith, N. H.},
+ YEAR = 2002,
+ TITLE = {Recombination in Animal Mitochondrial {DNA}},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 19,
+ PAGES = {2330-2332},
+ PDF = {maynardsmith2002.mbe.pdf},
+ DOI = {},
+ PMID = {12446825},
+ KEYWORDS = {recombination; mitochondria; Rana; Apodemus; Gammarus}
+ }
+
+ at ARTICLE{mcclellan2000,
+ AUTHOR = {McClellan, David A.},
+ YEAR = 2000,
+ TITLE = {The Phylogenetic Utility of the Codon-Degeneracy Model},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 51,
+ PAGES = {185-193},
+ PDF = {mcclellan2000.jme.pdf},
+ DOI = {10.1007/s002390010080},
+ PMID = {11029063},
+ KEYWORDS = {Codon-degeneracy model; phylogenetic reconstruction; Transition bias; Ancestral sequences}
+ }
+
+ at ARTICLE{mccracken1980,
+ AUTHOR = {McCracken, D. A. and Nadakavukaren, M. J.},
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+ PAGES = {39-44},
+ PDF = {mccracken1980.new-phytol.pdf},
+ DOI = {},
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+ KEYWORDS = {}
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+ at ARTICLE{mcdonald1998,
+ AUTHOR = {McDonald, John H.},
+ YEAR = 1998,
+ TITLE = {Improved Tests for Heterogeneity Across a Region of {DNA} Sequence in the Ratio of Polymorphism to Divergence},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 15,
+ PAGES = {377-384},
+ PDF = {mcdonald1998.mbe.pdf},
+ DOI = {},
+ PMID = {9549089},
+ KEYWORDS = {polymorphism; divergence; DNA sequence; natural selection}
+ }
+
+ at ARTICLE{mcglynn2002,
+ AUTHOR = {McGlynn, Peter and Lloyd, Robert G.},
+ YEAR = 2002,
+ TITLE = {Recombinational Repair and Restart of Damaged Replication Forks},
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+ PMID = {},
+ KEYWORDS = {}
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+ at ARTICLE{mcguire1997,
+ AUTHOR = {McGuire, G. and Wright, F. and Prentice, M. J.},
+ YEAR = 1997,
+ TITLE = {A Graphical Method for Detecting Recombination in Phylogenetic Data Sets},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 14,
+ PAGES = {1125-1131},
+ PDF = {mcguire1997.mpe.pdf},
+ DOI = {},
+ PMID = {9364770},
+ KEYWORDS = {graphical method; least squares; molecular evolution; Neisseria meningitidis; phylogeny; recombination}
+ }
+
+ at ARTICLE{mcguire1998,
+ AUTHOR = {McGuire, G. and Wright, F. and Prentice, M. J.},
+ YEAR = 1998,
+ TITLE = {{TOPAL}: recombination detection in {DNA} and protein sequences},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 14,
+ PAGES = {130-134},
+ PDF = {mcguire1998.bioinformatics.pdf},
+ DOI = {},
+ PMID = {9545456},
+ KEYWORDS = {recombination;; TOPAL}
+ }
+
+ at ARTICLE{mcguire2000,
+ AUTHOR = {McGuire, G. and Wright, F. and Prentice, M. J.},
+ YEAR = 2000,
+ TITLE = {{TOPAL} 2.0: improved detection of mosaic sequences within multiple alignments},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 16,
+ PAGES = {130-134},
+ PDF = {mcguire2000.bioinformatics.pdf},
+ DOI = {},
+ PMID = {10842734},
+ KEYWORDS = {recombination;; TOPAL}
+ }
+
+ at ARTICLE{mcguire2001,
+ AUTHOR = {McGuire, Grainne and Denham, Michael C. and Balding, David J.},
+ YEAR = 2001,
+ TITLE = {Models of Sequence Evolution for DNA Sequences Containing Gaps},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 18,
+ PAGES = {481-490},
+ PDF = {mcguire2001.mbe.pdf},
+ DOI = {},
+ PMID = {11264399},
+ KEYWORDS = {DNA sequences; evolution models; gaps; likelihood; Markov chain Monte Carlo; phylogenetics}
+ }
+
+ at ARTICLE{mckenzie2000,
+ AUTHOR = {McKenzie, Andy and Steel, Mike},
+ YEAR = 2000,
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+ JOURNAL = {Math. Biosci.},
+ VOLUME = 164,
+ PAGES = {81-92},
+ PDF = {mckenzie2000.math-biosci.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Trees; Phylogeny; Polya urn models; Yule model}
+ }
+
+ at ARTICLE{mckenzie2001,
+ AUTHOR = {McKenzie, Andy and Steel, Mike},
+ YEAR = 2001,
+ TITLE = {Properties of phylogenetic trees generated by Yule-type speciation models},
+ JOURNAL = {Math. Biosci.},
+ VOLUME = 170,
+ PAGES = {91-112},
+ PDF = {mckenzie2001.math-biosci.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Trees; Phylogeny; Speciation; Yule model; Maximum likelihood}
+ }
+
+ at ARTICLE{mclean1998,
+ AUTHOR = {McLean, Michael J. and Wolfe, Kenneth H. and Devine, Kevin M.},
+ YEAR = 1998,
+ TITLE = {Base Composition Skews, Replication Orientation, and Gene Order in 12 Prokaryote Genomes},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 47,
+ PAGES = {691-696},
+ PDF = {mclean1998.jme.pdf},
+ DOI = {},
+ PMID = {9847411},
+ KEYWORDS = {base composition; skews; replication orientation; gene orientation; Prokaryote genomes}
+ }
+
+ at ARTICLE{mcmorris1983,
+ AUTHOR = {McMorris, F. R. and Neumann, D. A.},
+ YEAR = 1983,
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+ JOURNAL = {Math. Soc. Sci},
+ VOLUME = 4,
+ PAGES = {131-136},
+ PDF = {hardcopy},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {Tree quasi-order; social welfare function; consensus}
+ }
+
+ at ARTICLE{mcmorris1983a,
+ AUTHOR = {McMorris, F. R. and Neumann, D. A.},
+ YEAR = 1983,
+ TITLE = {Additional Comments on Fitch and Smith's Conjecture for Minimal Length Trees},
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+ PAGES = {278},
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+ DOI = {},
+ PMID = {},
+ REMARK = {Comment on fitch1982},
+ KEYWORDS = {minimal trees; Hamiltonian circuits; evolutionary rates; maximum parsimony}
+ }
+
+ at ARTICLE{mcvean1999,
+ AUTHOR = {McVean, Gilean A.T. and Vieira, Jorge},
+ YEAR = 1999,
+ TITLE = {The Evolution of Codon Preferences in Drosophila: A Maximum-Likelihood Approach to Parameter Estimation and Hypothesis Testing},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 49,
+ PAGES = {63-75},
+ PDF = {mcvean1999.jme.pdf},
+ DOI = {},
+ PMID = {10368435},
+ KEYWORDS = {Codon preference; Drosophila; Maximum likelihood; Parameter estimation; Hypothesis testing}
+ }
+
+ at ARTICLE{mcvean2000,
+ AUTHOR = {McVean, Gilean A. T. and Hurst, Gregory D .D.},
+ YEAR = 2000,
+ TITLE = {Evolutionary Lability of Context-Dependent Codon Bias in Bacteria},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 50,
+ PAGES = {264-275},
+ PDF = {mcvean2000.jme.pdf},
+ DOI = {10.1007/s002399910031},
+ PMID = {10754070},
+ KEYWORDS = {Codon bias; Bacteria; Escherichia coli; Out-of-frame stop codons; AGG motifs; Haemophilus influenzae; Mycoplasma genitalium}
+ }
+
+ at ARTICLE{medina2001,
+ AUTHOR = {Medina, M\�{o}nica and Collins, Allen G. and Silberman, Jeffrey D. and Sogin, Mitchell L.},
+ YEAR = 2001,
+ TITLE = {Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit {rRNA}},
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+ KEYWORDS = {}
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+ at ARTICLE{megens2004,
+ AUTHOR = {Megens, Hendrik-Jan and van Moorsel, Coline H. M. and Piel, William H. and Pierce, Naomi E. and de Jong, Rienk},
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+ TITLE = {Tempo of speciation in a butterfly genus from the {Southeast} {Asian} tropics, inferred from mitochondrial and nuclear {DNA} sequence data},
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+ PAGES = {1181-1196},
+ PDF = {megens2004.mpe.pdf},
+ DOI = {10.1016/j.ympev.2003.10.002},
+ PMID = {},
+ KEYWORDS = {combined analysis; Rapid radiation; Hard polytomy; Molecular clock; Tropical diversity; Arhopala; Tempo of speciation; mitochondrial genes; nuclear genes}
+ }
+
+ at BOOK{mendel1990,
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+ AUTHOR = {Melkonian, Michael},
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+ at ARTICLE{messer1998,
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+ }
+
+ at ARTICLE{metzler2003,
+ AUTHOR = {Metzler, Dirk},
+ YEAR = 2003,
+ TITLE = {Statistical alignment based on fragment insertion and deletion models},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 19,
+ PAGES = {490-499},
+ PDF = {metzler2003.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg026},
+ PMID = {12611804},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{meunier2001,
+ AUTHOR = {Meunier, Julien and Eyre-Walker, Adam},
+ YEAR = 2001,
+ TITLE = {The Correlation Between Linkage Disequilibrium and Distance: Implications for Recombination in Hominid Mitochondria},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 18,
+ PAGES = {2132-2135},
+ PDF = {meunier2001.mbe.pdf},
+ DOI = {},
+ PMID = {11606711},
+ KEYWORDS = {Linkage Disequilibrium; Distance; Recombination; Mitochondria}
+ }
+
+ at ARTICLE{meyer1997,
+ AUTHOR = {Meyer, Trevor E. and Davis, James A. and Davidson, Jennifer L.},
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+ PDF = {meyer1997.jpdc.pdf},
+ DOI = {10.1006/jpdc.1997.1355},
+ PMID = {-},
+ KEYWORDS = {parallel computing; load balancing; runtime analysis; network of workstations}
+ }
+
+ at ARTICLE{meyer1999,
+ AUTHOR = {Meyer, Sonja and Weiss, Gunter and von Haeseler, Arndt},
+ YEAR = 1999,
+ TITLE = {Pattern of Nucleotide Substitution and Rate Heterogeneity in the Hypervariable Regions {I} and {II} of Human {mtDNA}},
+ JOURNAL = {Genetics},
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+ PDF = {meyer1999.genetics.pdf},
+ DOI = {},
+ PMID = {10388828},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{meyer2003,
+ AUTHOR = {Meyer, Sonja and von Haeseler, Arndt},
+ YEAR = 2003,
+ TITLE = {Identifying Site-Specific Substitution Rates},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = {20},
+ PAGES = {182-189},
+ PDF = {meyer2003.mbe.pdf},
+ DOI = {10.1093/molbev/msg019},
+ PMID = {12598684},
+ KEYWORDS = {sequence evolution; site specific substitution rates; maximum likelihood; tree reconstruction; human mitochondrial DNA}
+ }
+
+ at ARTICLE{mignone2004,
+ AUTHOR = {Mignone, Flavio and Horner, David S. and Pesole, Graziano},
+ YEAR = 2004,
+ TITLE = {{WebVar}: a resource for the rapid estimation of relative site variability from multiple sequence alignments},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 20,
+ PAGES = {1331-1333},
+ PDF = {mignone2004.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/bth076},
+ PMID = {},
+ KEYWORDS = {site specific rates; mutation rates; web interface}
+ }
+
+ at ARTICLE{miklos2004,
+ AUTHOR = {Mikl{\'o}s, I. and Lunter, G. A. and Holmes, I.},
+ YEAR = 2004,
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+ PAGES = {529-540},
+ PDF = {miklos2004.mbe.pdf},
+ DOI = {10.1093/molbev/msh043},
+ PMID = {14694074},
+ KEYWORDS = {Stochastic modeling of molecular evolution; Structural alignment; Maximum Likelihood evolutionary time estimation}
+ }
+
+ at ARTICLE{milinkovitch1997,
+ AUTHOR = {Milinkovitch, Michael C. and Lyons-Weiler, James},
+ YEAR = 1997,
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+ DOI = {10.1006/mpev.1998.0503},
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+ }
+
+ at ARTICLE{milinkovitch2004,
+ AUTHOR = {Milinkovitch, Michel C. and Caccone, Aldagisa and Amato, George},
+ YEAR = 2004,
+ TITLE = {Molecular phylogenetic analyses indicate extensive morphological convergence between the ''yeti'' and primates},
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+ PDF = {milinkovitch2004.mpe.pdf},
+ DOI = {10.1016/j.ympev.2004.01.009},
+ PMID = {},
+ KEYWORDS = {yeti; extensive morphological convergence; primates; Happy April Fool s Day!}
+ }
+
+ at ARTICLE{miller1997,
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+ at ARTICLE{miller2001,
+ AUTHOR = {Miller, Webb},
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+ TITLE = {Comparison of genomic {DNA} sequences: Solved and unsolved problems},
+ JOURNAL = {Bioinformatics},
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+ PDF = {miller2001.bioinformatics.pdf},
+ DOI = {},
+ PMID = {11331233},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{miller2002,
+ AUTHOR = {Miller, Richard E. and Buckley, Thomas R. and Manos, Paul S.},
+ YEAR = 2002,
+ TITLE = {An Examination of the Monophyly of Morning Glory Taxa Using {Bayesian} Phylogenetic Inference},
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+ PAGES = {740-753},
+ PDF = {miller2002.syst-biol.pdf},
+ DOI = {10.1080/10635150290102401},
+ PMID = {},
+ KEYWORDS = {Bayesian statistics; convergence; Ipomoea; Markov chain Monte Carlo; maximum likelihood; maximum parsimony; WAXY}
+ }
+
+ at ARTICLE{miller2003,
+ AUTHOR = {Miller, Crispin J. and Attwood, Teresa K.},
+ YEAR = 2003,
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+ PDF = {miller2003.nat-rev-mol-cell-biol.pdf},
+ DOI = {10.1038/nrm1013},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{miller2003a,
+ AUTHOR = {Miller, Jeremy A.},
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+ PAGES = {56-65},
+ PDF = {miller2003a.syst-biol.pdf},
+ DOI = {10.1080/10635150390132731},
+ PMID = {},
+ KEYWORDS = {Accuracy; combined data; comparative biology; congruence; data visualization; jackknife; pseudoreplicate; stability; support; total evidence}
+ }
+
+ at ARTICLE{milne2004,
+ AUTHOR = {Milne, Iain and Wright, Frank and Rowe, Glenn and Marshall, David F. and Husmeier, Dirk and McGuire, Gr{\'a}inne},
+ YEAR = 2004,
+ TITLE = {{TOPALi}: software for automatic identification of recombinant sequences within {DNA} multiple alignments},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 20,
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+ DOI = {10.1093/bioinformatics/bth155},
+ PMID = {},
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+ }
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+ at ARTICLE{mindell1996,
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+ }
+
+ at ARTICLE{mindell2001,
+ AUTHOR = {Mindell, David P. and Meyer, Axel},
+ YEAR = 2001,
+ TITLE = {Homology evolving},
+ JOURNAL = {TREE},
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+ DOI = {},
+ PMID = {},
+ KEYWORDS= {Partial homology; Genetic sex determination; Gametology; Exon shuffling; Pro-orthology; Lateral gene transfer; Paralogy; Synology; Orthology; Xenology; Gene duplication; Cladogenesis; Lineage merger}
+ }
+
+ at ARTICLE{mindell1999,
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+ }
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+ at ARTICLE{mira2002,
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+ at BOOK{mirkin1997,
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+ DOI = {},
+ PMID = {},
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+ }
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+ at ARTICLE{mitchison1999,
+ AUTHOR = {Mitchison, G. J.},
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+ }
+
+ at ARTICLE{miya2000,
+ AUTHOR = {Miya, Masaki and Nishida, Mutsumi},
+ YEAR = 2000,
+ TITLE = {Use of Mitogenomic Information in Teleostean Molecular Phylogenetics: A Tree-Based Exploration under the Maximum-Parsimony Optimality Criterion},
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+ PAGES = {437-455},
+ PDF = {miya2000.mpe.pdf},
+ DOI = {10.1006/mpev.2000.0839},
+ PMID = {11133198},
+ KEYWORDS = {mitogenomics; Teleostei; complete mtDNA sequence; long PCR; phylogenetic performance; taxonomic sampling; higher-level relationships}
+ }
+
+ at ARTICLE{miya2001,
+ AUTHOR = {Miya, Masaki and Kawaguchi, Akira and Nishida, Mutsumi},
+ YEAR = 2001,
+ TITLE = {Mitogenomic Exploration of Higher Teleostean Phylogenies: A Case Study for Moderate-Scale Evolutionary Genomics with 38 Newly Determined Complete Mitochondrial {DNA} Sequences},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 18,
+ PAGES = {1993-2009},
+ PDF = {miya2001.mbe.pdf},
+ DOI = {},
+ PMID = {11606696},
+ KEYWORDS = {mitogenomics; teleosts; complete mtDNA sequence; long PCR; taxonomic sampling; higher-level relationships}
+ }
+
+ at ARTICLE{miya2002,
+ AUTHOR = {Miya, Masaki and Takeshima, Hirohiko and Endo, Hiromitsu and Ishiguro, Naoya B. and Inoue, Jun G. and Mukai, Takahiko and Satoh, Takashi P. and Yamaguchi, Motoomi and Kawaguchi, Akira and Mabuchi, Kohji and Shirai, Shigeru M. and Nishida, Mutsumi},
+ YEAR = 2002,
+ TITLE = {Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial {DNA} sequences},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 26,
+ PAGES = {121-138},
+ PDF = {miya2002.mpe.pdf},
+ DOI = {10.1016/S1055-7903(02)00332-9},
+ PMID = {},
+ KEYWORDS = {Mitogenome; Actinopterygii; Ancient sh; Teleostei; Taxonomic sampling; Higher-level relationships}
+ }
+
+ at ARTICLE{miyamoto1995,
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+ }
+
+ at ARTICLE{moilanen1999,
+ AUTHOR = {Moilanen, Atte},
+ YEAR = 1999,
+ TITLE = {Searching for Most Parsimonious Trees with Simulated Evolutionary Optimization},
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+ DOI = {10.1006/clad.1998.0081},
+ PMID = {},
+ KEYWORDS = {fast bitwise logical operations; PARSIGAL; most parsimonious tree; evolutionary optimization; genetic programming; parsimony computer program}
+ }
+
+ at ARTICLE{moller2001,
+ AUTHOR = {M{\o}ller, Anders Pape and Jennions, Michael D.},
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+ }
+
+ at ARTICLE{moncalvo2002,
+ AUTHOR = {Moncalvo, Jean-Marc and Vilgalys, Rytas and Redhead, Scott A. and Johnson, James E. and James, Timothy Y. and Aime, M. Catherine and Hofstetter, Valerie and Verduin, Sebastiaan J. W. and Larsson, Ellen and Baroni, Timothy J. and Thorn, R. Greg and Jacobsson, Stig and Cl\'{e}men\c{c}on, Heinz and Miller, Jr., Orson K.},
+ YEAR = 2002,
+ TITLE = {One hundred and seventeen clades of euagarics},
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+ PAGES = {357-400},
+ PDF = {moncalvo2002.mpe.pdf},
+ DOI = {10.1016/S1055-7903(02)00027-1},
+ PMID = {},
+ KEYWORDS = {Nuclear large ribosomal subunit RNA; Phylogeny; Unequally weighted parismony; Agaricales; Homobasidiomycetes}
+ }
+
+ at ARTICLE{moncany1996,
+ AUTHOR = {Moncany, Maurice L. J. and Courtois, Pascal R. R.},
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+ }
+
+ at ARTICLE{moore1997,
+ AUTHOR = {Moore, William S.},
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+ biometrikaPDF = {moore1997.evol.pdf},
+ DOI = {},
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+ }
+
+ at ARTICLE{moore2004,
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+ DOI = {10.1016/j.parco.2003.12.005},
+ PMID = {},
+ KEYWORDS = {parallel computing; parallel bioinformatics; grid computing; scheduling;; Clusters; Genetic algorithms; Scheduling; Parallel genetic algorithms}
+ }
+
+ at ARTICLE{moran1951,
+ AUTHOR = {Moran, P. A. P.},
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+ }
+
+ at TECHREPORT{moret2000,
+ AUTHOR = {Moret, Bernard M. E. and St. John, Katherine and Vawter, Lisa and Warnow, Tandy},
+ YEAR = 2000,
+ TITLE = {An experimental study of the influence of quartet quality and sequence length on the performance of unweighted quartet-based and neighbor-joining phylogenetic reconstruction methods},
+ INSTITUTION = {University New Mexico},
+ ADDRESS = {Albuquerque, NM, USA},
+ TYPE = {UNM Computer Science Tech-Reports},
+ NUMBER = {TR-CS-2000-32},
+ PDF = {moret2000.TR-CS-2000-32.ps.gz},
+ KEYWORDS = {quartet quality; sequence length; performance; unweighted quartet-based methods; unweighted neighbor-joining methods}
+ }
+
+ at INPROCEEDINGS{moret2001,
+ AUTHOR = {Moret, Bernard M. E. and Bader, David A. and Warnow, Tandy},
+ YEAR = 2001,
+ TITLE = {High-Performance Algorithm Engineering for Computational Phylogenetics},
+ BOOKTITLE = {Proceedings of the ICCS 2001},
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+ PUBLISHER = {Springer Verlag},
+ PDF = {moret2001.ICCS2001.pdf},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {}
+ }
+
+ at TECHREPORT{moret2001a,
+ AUTHOR = {Moret, Bernard M. E. and Wang, Li-San and Warnow, Tandy},
+ YEAR = 2001,
+ TITLE = {New Software for Computational Phylogenetics},
+ INSTITUTION = {University New Mexico},
+ ADDRESS = {Albuquerque, NM, USA},
+ TYPE = {UNM Computer Science Tech-Reports},
+ NUMBER = {TR-CS-2001-35},
+ PDF = {moret2001a.TR-CS-2001-35.ps.gz},
+ KEYWORDS = {breakpoint phylogenies; dcm}
+ }
+
+ at ARTICLE{moret2002,
+ AUTHOR = {Moret, Bernard M. E. and Bader, David A. and Warnow, Tandy},
+ YEAR = 2002,
+ TITLE = {High-Performance Algorithm Engineering for Computational Phylogenetics},
+ JOURNAL = {J. Supercomput.},
+ VOLUME = 22,
+ PAGES = {99-111},
+ PDF = {moret2002.j-supercomput.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {high-performance computing; computational genomics; phylogeny reconstruction; breakpoint analysis; genome rearrangement; sorting by reversals}
+ }
+
+ at TECHREPORT{moret2002a,
+ AUTHOR = {Moret, Bernard M. E. and Roshan, Usman and Warnow, Tandy and Williams, Tiffani L.},
+ YEAR = 2002,
+ TITLE = {Performance of Supertree Methods on Various Dataset Decomposition},
+ INSTITUTION = {University New Mexico},
+ ADDRESS = {Albuquerque, NM, USA},
+ TYPE = {UNM Computer Science Tech-Reports},
+ NUMBER = {TR-CS-2002-39},
+ PDF = {moret2002a.TR-CS-2002-39.ps.gz},
+ KEYWORDS = {supertrees;; Supertree Methods; Various Dataset Decomposition; Performance}
+ }
+
+ at TECHREPORT{moret2003,
+ AUTHOR = {Moret, Bernard M. E. and Roshan, Usman and Williams, Tiffani L. and Warnow, Tandy},
+ YEAR = 2003,
+ TITLE = {Performance of Supertree Methods on Various Dataset Decomposition, II},
+ INSTITUTION = {University New Mexico},
+ ADDRESS = {Albuquerque, NM, USA},
+ TYPE = {UNM Computer Science Tech-Reports},
+ NUMBER = {TR-CS-2003-03},
+ PDF = {moret2003.TR-CS-2003-03.pdf},
+ KEYWORDS = {supertrees;; Supertree Methods; Various Dataset Decomposition; Performance}
+ }
+
+ at ARTICLE{morgan2001,
+ AUTHOR = {Morgan, David R.},
+ YEAR = 2001,
+ TITLE = {Decay analysis of large sets of phylogenetic data},
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+ }
+
+ at ARTICLE{morgenstern1999,
+ AUTHOR = {Morgenstern, Burkhard},
+ YEAR = 1999,
+ TITLE = {{DIALIGN} 2: improvement of the segment-to-segment approach to multiple sequence alignment},
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+ PAGES = {211-218},
+ PDF = {morgenstern1999.bioinformatics.pdf},
+ DOI = {},
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+ KEYWORDS = {multiple sequence alignment; DIALIGN}
+ }
+
+ at ARTICLE{morgenstern2002,
+ AUTHOR = {Morgenstern, Burkhard and Rinner, Oliver and Abdedda\"{\i}m, Sa\"{\i}d and Haase, Dirk and Mayer, Klaus F. X. and Dress, Andreas W. M. and Mewes, Hans-Werner},
+ YEAR = 2002,
+ TITLE = {Exon discovery by genomic sequence alignment},
+ JOURNAL = {Bioinformatics},
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+ KEYWORDS = {}
+ }
+
+ at ARTICLE{morgenstern2003,
+ AUTHOR = {Morgenstern, Burkhard and Goel, Sachin and Sczyrba, Alexander and Dress, Andreas},
+ YEAR = 2003,
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+ DOI = {10.1093/bioinformatics/btf882},
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+ KEYWORDS = {}
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+
+ at ARTICLE{moriyama1997,
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+ }
+
+ at ARTICLE{morrison2003,
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+ KEYWORDS = {Branch Lengths; Support; maximum likelihood; parsimony; PAUP*; DNAML}
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+ KEYWORDS = {Hantavirus; Evolution; Host switching}
+ }
+
+ at ARTICLE{nemirov2003,
+ AUTHOR = {Nemirov, Kirill and Henttonen, Heikki and Vaheri, Antti and Plyusnin, Alexander},
+ YEAR = 2003,
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+ PAGES = {125-126},
+ PDF = {nemirov2003.virus-res.pdf},
+ DOI = {10.1016/S0168-1702(02)00320-9},
+ PMID = {},
+ KEYWORDS = {Hantavirus; Evolution; Host switching}
+ }
+
+ at PHDTHESIS{nemirov2003a,
+ AUTHOR = {Nemirov, Kirill},
+ YEAR = 2003,
+ TITLE = {Genetic Relationships of Saaremaa and Dobrava Hantaviruses},
+ SCHOOL = {University of Helsinki},
+ ADDRESS = {Finland},
+ PDF = {nemirov2003a.phdthesis.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Saarema; Dobrava; Hantavirus}
+ }
+
+ at ARTICLE{nemirov2004,
+ AUTHOR = {Nemirov, Kirill and Andersen, Hans K. and Leirs, Herwig and Henttonen, Heikki and Vaheri, Antti and Lundkvist, {\o{A}}ke and Plyusnin, Alexander},
+ YEAR = 2004,
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+ PDF = {nemirov2004.j-clin-virol.pdf},
+ DOI = {10.1016/j.jcv.2003.12.009},
+ PMID = {},
+ KEYWORDS = {Hantavirus; Genotype; Molecular epidemiology; Dobrava; Saarema; Denmark}
+ }
+
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+ YEAR = 2003,
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+ KEYWORDS = {Ancestral character state reconstruction; biogeography; ETS; Hawaii; island evolution; ITS; molecular systematics; Psychotria; Comparison; Parsimony; Likelihood Approaches}
+ }
+
+ at ARTICLE{ness2002,
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+ }
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+ KEYWORDS = {Complete mitochondrial DNAs; Mammalian phylogeny; Chiroptera; Flying fox; Monophyly; Divergence time}
+ }
+
+ at ARTICLE{nikaido2001,
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+ }
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+ }
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+ KEYWORDS = {gene discovery; false discoveries; criteria; models}
+ }
+
+ at BOOK{oram1991,
+ AUTHOR = {Oram, Andrew and Talbott, Steve},
+ YEAR = 1991,
+ TITLE = {Managing Projects with make},
+ EDITION = 2,
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+
+ at ARTICLE{osborne2002,
+ AUTHOR = {Osborne, M. J. and Christidis, L. and Norman, J. A.},
+ YEAR = 2002,
+ TITLE = {Molecular phylogenetics of the {Diprotodontia} (kangaroos, wombats, koala, possums, and allies)},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 25,
+ PAGES = {219-228},
+ PDF = {osborne2002.mpe.pdf},
+ DOI = {10.1016/S1055-7903(02)00252-X},
+ PMID = {},
+ KEYWORDS = {Diprotodontia; mammalia; marsupials; ND2}
+ }
+
+ at ARTICLE{ota2000,
+ AUTHOR = {Ota, Satoshi and Li, Wen-Hsiung},
+ YEAR = 2000,
+ TITLE = {{NJML}: A Hybrid Algorithm for the Neighbor-Joining and Maximum-Likelihood Methods},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 17,
+ PAGES = {1401-1409},
+ PDF = {ota2000.mbe.pdf},
+ DOI = {},
+ PMID = {10958856},
+ KEYWORDS = {phylogenetic reconstruction; topology search; subtrees; greedy algorithm}
+ }
+
+ at ARTICLE{ota2000a,
+ AUTHOR = {Ota, Rissa and Waddell, Peter J. and Hasegawa, Masami and Shimodaira, Hidetoshi and Kishino, Hirohira},
+ YEAR = 2000,
+ TITLE = {Appropriate Likelihood Ratio Tests and Marginal Distributions for Evolutionary Tree Models with Constraints on Parameters},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 17,
+ PAGES = {798-803},
+ PDF = {ota2000a.mbe.pdf},
+ DOI = {},
+ PMID = {10779540},
+ KEYWORDS = {Phylogenetic log likelihood ratio tests; truncated or half-normal distributions; mixed chi-square; gamma site substitution rate heterogeneity}
+ }
+
+ at ARTICLE{ota2001,
+ AUTHOR = {Ota, Satoshi and Li, Wen-Hsiung},
+ YEAR = 2000,
+ TITLE = {{NJML+}: An Extension of the {NJML} Method to Handle Protein Sequence Data and Computer Software Implementation},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 18,
+ PAGES = {1983-1992},
+ PDF = {ota2001.mbe.pdf},
+ DOI = {},
+ PMID = {11606695},
+ KEYWORDS = {tree reconstruction; topology search; approximate likelihood; neighbor joining; likelihood test}
+ }
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+ at BOOK{ottmann1990,
+ AUTHOR = {Ottmann, Thomas and Widmayer, Peter},
+ YEAR = 1990,
+ TITLE = {{Algorithmen} und {Datenstrukturen}},
+ PUBLISHER = {BI Wissenschaftsverlag},
+ ADDRESS = {Mannheim},
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+ KEYWORDS = {}
+ }
+
+ at BOOK{ottmann1993,
+ AUTHOR = {Ottmann, Thomas and Widmayer, Peter},
+ YEAR = 1993,
+ TITLE = {{Algorithmen} und {Datenstrukturen}},
+ EDITION = 2,
+ PUBLISHER = {BI Wissenschaftsverlag},
+ ADDRESS = {Mannheim},
+ ISBN = {3-411-16602-9},
+ KEYWORDS = {}
+ }
+
+ at BOOK{ottmann1996,
+ AUTHOR = {Ottmann, Thomas and Widmayer, Peter},
+ YEAR = 1996,
+ TITLE = {{Algorithmen} und {Datenstrukturen}},
+ EDITION = 3,
+ PUBLISHER = {Spektrum Akademischer Verlag},
+ ADDRESS = {Heidelberg},
+ ISBN = {3-827-40110-0},
+ KEYWORDS = {}
+ }
+
+ at BOOK{ottmann2002,
+ AUTHOR = {Ottmann, Thomas and Widmayer, Peter},
+ YEAR = 2002,
+ TITLE = {{Algorithmen} und {Datenstrukturen}},
+ EDITION = 4,
+ PUBLISHER = {Spektrum Akademischer Verlag},
+ ADDRESS = {Heidelberg},
+ ISBN = {3-827-41029-0},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{otto2003,
+ AUTHOR = {Ottp, Sarah P.},
+ YEAR = 2003,
+ TITLE = {In polyploids, one plus one does not equal two},
+ JOURNAL = {TREE},
+ VOLUME = 18,
+ PAGES = {431-433},
+ PDF = {otto2003.tree.pdf},
+ DOI = {10.1016/S0169-5347(03)00213-1},
+ PMID = {},
+ KEYWORDS = {polyploids, missing copies}
+ }
+
+ at ARTICLE{otu2003,
+ AUTHOR = {Otu, Hasan H. and Sayood, Khalid},
+ YEAR = 2003,
+ TITLE = {A new sequence distance measure for phylogenetic tree construction},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 19,
+ PAGES = {2122-2130},
+ PDF = {otu2003.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg295},
+ PMID = {},
+ KEYWORDS = {sequence distance measure; phylogenetic tree construction; compression; Lempel-Ziv complexity}
+ }
+
+ at BOOK{oualline2001,
+ AUTHOR = {Oualline, Steve},
+ YEAR = 2001,
+ TITLE = {{Vi IMproved} -- {Vim}},
+ PUBLISHER = {New Riders},
+ ADDRESS = {Berkeley, CA, USA},
+ PDF = {books/oualline2001.VIM.book.pdf},
+ ISBN = {0735710015},
+ KEYWORDS = {VIM; editor}
+ }
+
+ at ARTICLE{oudshoorn2002,
+ AUTHOR = {Oudshoorn, Michael J. and Huang, Lin},
+ YEAR = 2002,
+ TITLE = {Evolving toward an Optimal Scheduling Solution through Adaptivity},
+ JOURNAL = {J. Parallel Distrib. Comput.},
+ VOLUME = 62,
+ PAGES = {1203-1222},
+ PDF = {oudshoorn2002.jpdc.pdf},
+ DOI = {10.1006/jpdc.2002.1844},
+ PMID = {},
+ KEYWORDS = {parallel computing; Scheduling; Adaptivity}
+ }
+
+ at ARTICLE{ouzounis2003,
+ AUTHOR = {Ouzounis, Christos A. and Valencia, Alfonso},
+ YEAR = 2003,
+ TITLE = {Early bioinformatics: the birth of a discipline -- a personal view},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 19,
+ PAGES = {2176-2190},
+ PDF = {ouzounis2003.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg309},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{ovcharenko2004,
+ AUTHOR = {Ovcharenko, Ivan and Boffelli, Dario and Loots, Gabriela G.},
+ YEAR = 2004,
+ TITLE = {{eShadow}: A Tool for Comparing Closely Related Sequences},
+ JOURNAL = {Genome Res.},
+ VOLUME = 14,
+ PAGES = {1191-1198},
+ PDF = {ovcharenko2004.genome-res.pdf},
+ DOI = {10.1101/gr.1773104},
+ PMID = {15173121},
+ KEYWORDS = {sequence comparison; closely related sequences}
+ }
+
+
+ at ARTICLE{paabo2000,
+ AUTHOR = {P\"a\"abo, Swante},
+ YEAR = 2000,
+ TITLE = {Human Evolution},
+ JOURNAL = {TIBS},
+ VOLUME = 24,
+ PAGES = {M13-M15},
+ NOTE = {Millenium Issue of TCB (9), TIBS (24), and TIG (15)},
+ PDF = {paabo2000.tibs.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{packer2003,
+ AUTHOR = {Packer, Alan},
+ YEAR = 2003,
+ TITLE = {Evolutionary Genomics: Splicing and evolutionary change},
+ JOURNAL = {Nat. Rev. Genet.},
+ VOLUME = 4,
+ PAGES = {401},
+ PDF = {packer2003.nrg.pdf},
+ DOI = {doi:10.1038/nrg1103},
+ PMID = {},
+ KEYWORDS = {Splicing; evolutionary change}
+ }
+
+ at ARTICLE{padidam1999,
+ AUTHOR = {Padidam, Malla and Sawyer, Stanley and Fauquet, Claude M.},
+ YEAR = 1999,
+ TITLE = {Possible Emergence of New {Geminiviruses} by Frequent Recombination},
+ JOURNAL = {Virology},
+ VOLUME = 265,
+ PAGES = {218-225},
+ PDF = {padidam1999.virology.pdf},
+ DOI = {10.1006/viro.1999.0056},
+ PMID = {10600594},
+ KEYWORDS = {recombination;; Geminiviruses; Frequent Recombination}
+ }
+
+ at ARTICLE{page1989,
+ AUTHOR = {Page, Roderic D. M.},
+ YEAR = 1989,
+ TITLE = {Comments on component-compatibility in historical biogeography},
+ JOURNAL = {Cladistics},
+ VOLUME = 5,
+ PAGES = {167-182},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{page1996,
+ AUTHOR = {Page, Roderic D. M.},
+ YEAR = 1996,
+ TITLE = {{TreeView}: An application to display phylogenetic trees on personal computers},
+ JOURNAL = {Comput. Appl. Biosci.},
+ VOLUME = 12,
+ PAGES = {357-358},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{page1996a,
+ AUTHOR = {Page, Roderic D. M.},
+ YEAR = 1996,
+ TITLE = {On consensus, confidence, and ``total'' evidence},
+ JOURNAL = {Cladistics},
+ VOLUME = 12,
+ PAGES = {83-92},
+ PDF = {page1996a.cladistics.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{page1997,
+ AUTHOR = {Page, Roderic D. M. and Charleston, Michael A.},
+ YEAR = 1997,
+ TITLE = {From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 7,
+ PAGES = {231-240},
+ PDF = {page1997.mpe.pdf},
+ DOI = {10.1006/mpev.1996.0390},
+ PMID = {9126565},
+ KEYWORDS = {gene duplication; loss; lineage sorting; incongruence; reconciled trees; gene tree with respect to species tree; relationship between trees}
+ }
+
+ at INCOLLECTION{page1997a,
+ AUTHOR = {Page, Roderic D. M. and Charleston, Michael A.},
+ YEAR = 1997,
+ TITLE = {Reconciled trees and incongruent gene and species trees},
+ EDITOR = {Mirkin, B. and McMorris, F. R. and Roberts, F. S. and Rzhetsky A.},
+ BOOKTITLE = {Mathematical hierarchies in biology},
+ SERIES = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
+ VOLUME = 37,
+ PUBLISHER = {American Mathematical Society},
+ PAGES = {57-70},
+ PDF = {page1997a.math-hier-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {gene tree; heuristic search; phylogeny; reconciled tree}
+ }
+
+ at BOOK{page1998,
+ AUTHOR = {Page, Roderic D. M. and Holmes, Edward C.},
+ YEAR = 1998,
+ TITLE = {Molecular Evolution: A Phylogenetic Approach},
+ PUBLISHER = {Blackwell Science},
+ ADDRESS = {Oxford}
+ }
+
+ at ARTICLE{page1998a,
+ AUTHOR = {Page, Roderic D. M.},
+ YEAR = 1998,
+ TITLE = {{GeneTree}: Comparing gene and species phylogenies using reconciled
+ trees},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 14,
+ PAGES = {819-920},
+ PDF = {page1998a.bioinformatics.pdf},
+ DOI = {},
+ PMID = {9918954},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{page1998b,
+ AUTHOR = {Page, Roderic D. M. and Charleston, Michael A.},
+ YEAR = 1998,
+ TITLE = {Trees within trees: Phylogeny and historical associations},
+ JOURNAL = {TREE},
+ VOLUME = 13,
+ PAGES = {356-359},
+ PDF = {page1998b.tree.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {reconciled trees; phylogeny; biogeography; coevolution; gene trees; molecular evolution; horizontal transfer; historical associations}
+ }
+
+ at ARTICLE{page1998c,
+ AUTHOR = {Page, Roderic D. M. and Lee, P. L. M. and Becher, S. A. and Griffiths, R. and Clayton, D. H.},
+ YEAR = 1998,
+ TITLE = {A different tempo of mitochondrial {DNA} evolution in birds and their parasitic lice},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 9,
+ PAGES = {276-293},
+ PDF = {page1998c.mpe.pdf},
+ DOI = {10.1006/mpev.1997.0458},
+ PMID = {9562986},
+ KEYWORDS = {mitochondrial cytochrome b; cospeciation; three times more rapid evolution of parasides; small effective population sizes}
+ }
+
+ at ARTICLE{page1999,
+ AUTHOR = {Page, Roderic D. M. and Charleston, Michael A.},
+ YEAR = 1999,
+ TITLE = {Comments on Allard and Carpenter (1996), or the ``aquatic ape'' hypothesis revisited},
+ JOURNAL = {Cladistics},
+ VOLUME = 15,
+ PAGES = {73-74},
+ PDF = {page1999.cladistics.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{page2000,
+ AUTHOR = {Page, Roderic D. M.},
+ YEAR = 2000,
+ TITLE = {Extracting Species Trees From Complex Gene Trees: Reconciled Trees And Vertebrate Phylogeny},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 14,
+ PAGES = {89-106},
+ PDF = {page2000.mpe.pdf},
+ DOI = {10.1006/mpev.1999.0676},
+ PMID = {10631044},
+ KEYWORDS = {Species Trees; Complex Gene Trees; Reconciled Trees; Vertebrate Phylogeny}
+ }
+
+ at TECHREPORT{page2000a,
+ AUTHOR = {Page, Roderic D. M.},
+ YEAR = 2000,
+ TITLE = {On The Dangers Of Aligning {RNA} Sequences Using ``Conserved'' Motifs},
+ TYPE = {Technical Reports in Taxonomy},
+ INSTITUTION = {University of Glasgow},
+ NUMBER = {00-01},
+ PDF = {page2000.tech-rep-tax.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {rRNA secondary structure; multiple alignment; 12S rRNA; insects; lice; tree comparison metrics}
+ }
+
+ at MANUAL{page2001,
+ AUTHOR = {Page, Roderic D. M. and Cotton, James A.},
+ YEAR = 2001,
+ TITLE = {Genetree : A Tool for Exploring Gene Family Evolution},
+ ORGANIZATION = {Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, University of Glasgow},
+ ADDRESS = {Glasgow G12 8QQ, UK},
+ PDF = {page2001.genetree.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at INPROCEEDINGS{page2002,
+ AUTHOR = {Page, Roderic D. M. and Cotton, James A.},
+ YEAR = 2002,
+ TITLE = {Vertebrate phylogenomics: Reconciled trees and gene duplications},
+ BOOKTITLE = {Proceedings of the 6th Pacific Symposium on Biocomputing (PSB 2002)},
+ PAGES = {536-547},
+ MONTH = {January},
+ ADDRESS = {Hawaii},
+ PDF = {page2002.PSB2002.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at TECHREPORT{page2002a,
+ AUTHOR = {Page, Roderic D. M. and Cruickshank, Robert and Johnson, Kevin P.},
+ YEAR = 2002,
+ TITLE = {{Louse} ({Insecta}: {Phthiraptera}) mitochondrial {12S} {rRNA} secondary structure is highly variable},
+ TYPE = {Technical Reports in Taxonomy},
+ INSTITUTION = {University of Glasgow},
+ NUMBER = {02-01},
+ PDF = {page2002a.tech-rep-tax.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {rRNA secondary structure; multiple alignment; 12S rRNA; insects; lice; tree comparison metrics}
+ }
+
+ at INCOLLECTION{page2002b,
+ AUTHOR = {Page, Roderic D. M.},
+ TITLE = {Introduction to Inferring Evolutionary Relationships},
+ YEAR = 2002,
+ PAGES = {6.1.1-6.1.3},
+ EDITOR = {Baxevanis, Andreas D. and Davison, Daniel B. and Page, Roderic D. M. and Stormo, Gary and Stein, Lincoln},
+ BOOKTITLE = {Current Protocols in Bioinformatics},
+ PUBLISHER = {Wiley and Sons},
+ ADDRESS = {New York, USA},
+ PDF = {page2002b.cpbi-61-manuscript.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at INCOLLECTION{page2002c,
+ AUTHOR = {Page, Roderic D. M.},
+ TITLE = {Visualising Phylogenetic Trees Using TreeView},
+ YEAR = 2002,
+ PAGES = {6.2.1-6.2.15},
+ EDITOR = {Baxevanis, Andreas D. and Davison, Daniel B. and Page, Roderic D. M. and Stormo, Gary and Stein, Lincoln},
+ BOOKTITLE = {Current Protocols in Bioinformatics},
+ PUBLISHER = {Wiley and Sons},
+ ADDRESS = {New York, USA},
+ PDF = {page2002c.cpbi-62-manuscript.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at INPROCEEDINGS{page2002d,
+ AUTHOR = {Page, Roderic D. M.},
+ YEAR = 2002,
+ TITLE = {Modified Mincut Supertrees},
+ BOOKTITLE = {Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI 2002)},
+ SERIES = {Lecture Notes in Computer Science},
+ VOLUME = 2452,
+ PAGES = {537-551},
+ PUBLISHER = {Springer},
+ ADDRESS = {New York},
+ PDF = {page2002d.LNCS-TR.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Modified MinCutSupertree; supertree}
+ }
+
+ at TECHREPORT{page2002e,
+ AUTHOR = {Page, Roderic D. M. and Charleston, Michael A.},
+ YEAR = 2002,
+ TITLE = {Treemap Versus BPA (Again): A Response To Dowling},
+ INSTITUTION = {Taxonomy, Systematics, and Bioinformatics at the University of Glasgow},
+ ADDRESS = {Glasgow, UK},
+ TYPE = {Technical Reports in Taxonomy},
+ NUMBER = {02-02},
+ PDF = {page2002e.TR-02-02.pdf},
+ KEYWORDS = {TreeMap; BPA; Brooks Parsimony Analysis}
+ }
+
+ at INCOLLECTION{page2004,
+ AUTHOR = {Page, Roderic D. M.},
+ TITLE = {Taxonomy, supertrees, and the Tree of Life},
+ YEAR = 2004,
+ PAGES = {in press},
+ EDITOR = {Bininda-Emonds, Olaf R. P.},
+ BOOKTITLE = {Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life},
+ PUBLISHER = {Kluwer Academic},
+ ADDRESS = {Dordrecht, The Netherlands},
+ PDF = {page2004.supertrees.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertrees;; MinCutSupertree; taxonomy; cluster graphs; classification graphs; constraints}
+ }
+
+ at INCOLLECTION{page2004a,
+ AUTHOR = {Page, Roderic D. M.},
+ TITLE = {Phyloinformatics: Towards a Phylogenetic Database},
+ YEAR = 2004,
+ PAGES = {in press},
+ EDITOR = {Jason Wang, et al.},
+ BOOKTITLE = {Data Mining in Bioinformatics},
+ PUBLISHER = {ACM Press},
+ ADDRESS = {New York, NY, USA},
+ PDF = {page2004a.mining.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {phylogenetic database;; }
+ }
+
+
+ at ARTICLE{pagel2000,
+ AUTHOR = {Pagel, Mark},
+ YEAR = 2000,
+ TITLE = {Phylogenetic-evolutionary approaches to bioinformatics},
+ JOURNAL = {Brief. Bioinform.},
+ VOLUME = 1,
+ PAGES = {117-130},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {bioinformatics; comparative methods; phylogeny; molecular evolution; adaptation}
+ }
+
+ at ARTICLE{palenik1992,
+ AUTHOR = {Palenik, B. and Haselkorn, R.},
+ YEAR = 1992,
+ TITLE = {Multiple evolutionary origins of prochlorophytes, chlorophyll b--containing prokaryotes},
+ JOURNAL = {Nature},
+ VOLUME = 355,
+ PAGES = {265-267},
+ PDF = {NICHT VORHANDEN},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{panda1997,
+ AUTHOR = {Panda, Dhabaleswar K. and Ni, Lionel M.},
+ YEAR = 1997,
+ TITLE = {Special Issue on Workstation Clusters and Network-Based Computing},
+ JOURNAL = {J. Parallel Distrib. Comput.},
+ VOLUME = 43,
+ PAGES = {63-64},
+ PDF = {panda1997.jpdc.pdf},
+ DOI = {10.1006/jpdc.1997.1331},
+ PMID = {-},
+ KEYWORDS = {parallel computing; Workstation Clusters; Network-Based Computing}
+ }
+
+ at ARTICLE{pandit2004,
+ AUTHOR = {Pandit, Shashi B. and Bhadra, Rana and Gowri, V.S. and Balaji, S. and and Anand, B. and Srinivasan, N.},
+ YEAR = 2004,
+ TITLE = {{SUPFAM}: A database of sequence superfamilies of protein domains},
+ JOURNAL = {BMC Bioinformatics},
+ VOLUME = 5,
+ PAGES = {28},
+ PDF = {pandit2004.bmc-bioinformatics-manuscript.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {database; superfamilies; protein domains}
+ }
+
+ at ARTICLE{paradis1998,
+ AUTHOR = {Paradis, Emmanuel},
+ YEAR = 1998,
+ TITLE = {Testing for Constant Diversification Rates Using Molecular Phylogenies: A General Approach Based on Statistical Tests for Goodness of Fit},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 15,
+ PAGES = {476-479},
+ PDF = {paradis1998.mbe.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {diversification; goodness of fit; null models; phylogeny}
+ }
+
+ at ARTICLE{paradis2004,
+ AUTHOR = {Paradis, Emmanuel and Claude, Julien and Strimmer, Korbinian},
+ YEAR = 2004,
+ TITLE = {{APE}: Analyses of Phylogenetics and Evolution in {R} language},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 20,
+ PAGES = {289-290},
+ PDF = {paradis2004.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg412},
+ PMID = {14734327},
+ KEYWORDS = {R-project; Phylogenetics; Evolution}
+ }
+
+ at ARTICLE{paraskevis2003,
+ AUTHOR = {Paraskevis, D. and Lemey, P. and Salemi, M. and Van de Peer, Y. and Vandamme, A.-M.},
+ YEAR = 2003,
+ TITLE = {Analysis of the Evolutionary Relationships of {HIV-1} and {SIVcpz} Sequences Using {Bayesian} Inference: Implications for the Origin of {HIV-1}},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 20,
+ PAGES = {1986-1996},
+ PDF = {paraskevis2003.mbe.pdf},
+ DOI = {10.1093/molbev/msg207},
+ PMID = {12949143},
+ KEYWORDS = {HIV; SIVcpz; evolution; Bayesian inference}
+ }
+
+ at ARTICLE{patnaik1950,
+ AUTHOR = {Patnaik, P. B.},
+ YEAR = 1950,
+ TITLE = {The Use of Mean Range as an Estimator of Variance in Statistical Tests},
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+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Mean Range; Estimator of Variance; Statistical Tests}
+ }
+
+ at TECHREPORT{pattison2001,
+ AUTHOR = {Pattison, Tim and Vernik, Rudi and Phillips, Matthew},
+ YEAR = 2001,
+ MONTH = {August},
+ TITLE = {Information Visualisation using Composable Layouts and Visual Sets},
+ INSTITUTION = {Defence Science \& Technology Organisation},
+ ADDRESS = {Edinburgh, South Australia},
+ TYPE = {Research Report},
+ NUMBER = {DSTO-RR-0216},
+ PDF = {pattison2001.DSTO-RR-0216.pdf},
+ KEYWORDS = {},
+ NOTE = {http://www.dsto.defence.gov.au/corporate/reports/DSTO-RR-0216.pdf}
+ }
+
+ at MASTERSTHESIS{paulsen2003,
+ AUTHOR = {Paulsen, Ingo},
+ TITLE = {Genb{\"a}ume in Vertebraten},
+ YEAR = 2003,
+ SCHOOL = {Universit{\"a}t D{\"u}sseldorf},
+ TYPE = {Diplomarbeit},
+ PDF = {paulsen2003.diplom.pdf},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{pauplin2000,
+ AUTHOR = {Pauplin, Yves},
+ YEAR = 2000,
+ TITLE = {Direct Calculation of a Tree Length Using a Distance Matrix},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 51,
+ PAGES = {41-47},
+ PDF = {pauplin2000.jme.pdf},
+ DOI = {10.1007/s002390010065},
+ PMID = {10903371},
+ KEYWORDS = {Phylogenetic trees; Distance matrix; Minimum-evolution method; Least square estimates; Cetacean phylogeny; Tree rooting}
+ }
+
+ at ARTICLE{pavesi1999,
+ AUTHOR = {Pavesi, Angelo},
+ YEAR = 1999,
+ TITLE = {Relationships Between Transcriptional and Translational Control of Gene Expression in {Saccharomyces} cerevisiae: A Multiple Regression Analysis},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 48,
+ PAGES = {133-141},
+ PDF = {pavesi1999.jme.pdf},
+ DOI = {},
+ PMID = {9929381},
+ KEYWORDS = {Yeast genome; mRNA sequence evo-lution; Codon usage bias; Gene expression; Sta-tistical model; Small open reading frames}
+ }
+
+ at ARTICLE{pearson1995,
+ AUTHOR = {Pearson, William R.},
+ TITLE = {Comparison of methods for searching protein sequence databases},
+ JOURNAL = {Protein Sci.},
+ YEAR = 1995,
+ VOLUME = 4,
+ PAGES = {1145-1160},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {BLAST; FASTA; PAM250; sequence similarity; Smith-Waterman}
+ }
+
+ at ARTICLE{pearson1988,
+ AUTHOR = {Pearson, William R. and Lipman, David J.},
+ TITLE = {Improved tools for biological sequence comparison},
+ JOURNAL = {Proc. Natl. Acad. Sci. USA},
+ YEAR = 1988,
+ VOLUME = 85,
+ PAGES = {2444-2448},
+ PDF = {pearson1988.pnas.pdf},
+ DOI = {},
+ PMID = {3162770},
+ KEYWORDS = {amino acid; nucleic acid; data base searches; local similarity}
+ }
+
+ at ARTICLE{pearson1999,
+ AUTHOR = {Pearson, William R. and Robins, Gabriel and Zhang, Tongtong},
+ TITLE = {Generalized Neighbor--Joining: More Reliable Phylogenetic Tree Reconstruction},
+ JOURNAL = {Mol. Biol. Evol.},
+ YEAR = 1999,
+ VOLUME = 16,
+ PAGES = {806-816},
+ PDF = {pearson1999.mbe.pdf},
+ DOI = {},
+ PMID = {10368958},
+ KEYWORDS = {phylogenetic reconstruction; neighbor-joining; least-squares; minimal evolution; solution space sampling}
+ }
+
+ at MISC{pearson2000,
+ AUTHOR = {Pearson, William R.},
+ YEAR = 2000,
+ MONTH = {},
+ TITLE = {Protein sequence comparison and Protein evolution},
+ HOWPUBLISHED = {Tutorial given at the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB 2000)},
+ NOTE = {Handout},
+ PDF = {pearson2000.ISMB-tutorial.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Protein sequence comparison; Protein evolution; Alignment methods; statistics of sequence similarity scores; Identifying distantly related protein sequences; Repeated structures in proteins}
+ }
+
+ at ARTICLE{pebusque1998,
+ AUTHOR = {P\'{e}busque, Marie-Jos\'{e}phe and Coulier, Fran\c{c}ois and Birnbaum, Daniel and Pontarotti, Pierre},
+ YEAR = 1998,
+ TITLE = {Ancient Large-Scale Genome Duplications: Phylogenetic and Linkage Analyses Shed Light on Chordate Genome Evolution },
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 15,
+ PAGES = {1145-1159},
+ PDF = {pebusque1998.mbe.pdf},
+ DOI = {},
+ PMID = {9729879},
+ KEYWORDS = {Caenorhabditis elegans; Drosophila melanogaster; evolution; gene duplication; genome; Homo sapiens}
+ }
+
+ at ARTICLE{pedersen1998,
+ AUTHOR = {A. K. Pedersen and C. Wiuf and F. B. Christiansen},
+ YEAR = 1998,
+ TITLE = {A codon-based model designed to describe lentiviral evolution},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 15,
+ PAGES = {1069-1081}
+ }
+
+ at PHDTHESIS{pedersen1999,
+ AUTHOR = {Pedersen, Christian N{\o}rgaard Storm},
+ YEAR = 1999,
+ TITLE = {Algorithms in Computational Biology},
+ SCHOOL = {University of Aarhus},
+ ADDRESS = {Aarhus, Denmark},
+ PDF = {pedersen1999.thesis.pdf}
+ }
+
+ at INPROCEEDINGS{pedretti1999,
+ AUTHOR = {Pedretti, K. T. and Casavant, T. L. and Braun, R. C. and Scheetz, T. E. and Birkett, C. L. and Roberts, C. A.},
+ YEAR = 1999,
+ TITLE = {Three Complementary Approaches to Parallelization of Local {BLAST} Service on Workstation Clusters},
+ BOOKTITLE = {Proceedings of the 5th International Conference on Parallel Computing Technologies (PaCT-99)},
+ SERIES = {Lecture Notes in Computer Science},
+ VOLUME = 1662,
+ PAGES = {271-282},
+ PUBLISHER = {Springer},
+ ADDRESS = {New York},
+ PDF = {pedretti1999.LNCS.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel computing; parallel bioinformatics; multithreading; dynamic programming; sequence comparison; BLAST}
+ }
+
+ at INPROCEEDINGS{pedretti1999a,
+ AUTHOR = {Pedretti, Kevin T. and Casavant, Thomas L. and Braun, R. C. and Scheetz, Todd E. and Birkett, C. L. and Roberts, Chad A.},
+ YEAR = 1999,
+ TITLE = {Three Complementary Approaches to Parallelization of Local {BLAST} Service on Workstation Clusters (invited paper)},
+ BOOKTITLE = {Proceedings of the 5th International Conference on Parallel Computing Technologies (PaCT 1999), September 6-10, St. Petersburg, Russia},
+ PAGES = {311-322},
+ SERIES = {Lecture Notes in Computer Science},
+ PUBLISHER = {Springer},
+ ADRESS = {Heidelberg},
+ VOLUME = {1662},
+ PDF = {pedretti1999a.lncs.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing; multithreading; dynamic programming; sequence comparison}
+ }
+
+ at ARTICLE{peer1994,
+ AUTHOR = {Van de Peer, Yves and De Wachter, Rupert},
+ YEAR = 1994,
+ TITLE = {{TREECON} for {Windows}: A software package for the construction and drawing of evolutionary trees for the {Microsoft} {Windows} environment},
+ JOURNAL = {Comput. Appl. Biosci.},
+ VOLUME = 10,
+ PAGES = {569-570},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{peer1994a,
+ AUTHOR = {Van de Peer, Yves and Van den Broeck, I. and De Wachter, Rupert},
+ YEAR = 1994,
+ TITLE = {Database on structure of small ribosomal subunit {RNA} sequences},
+ JOURNAL = {Nucleic Acids Res.},
+ VOLUME = 22,
+ PAGES = {3488-3494},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{peer1996,
+ AUTHOR = {Van de Peer, Yves and Van der Auwera, Gert and De Wachter, Rupert},
+ YEAR = 1996,
+ TITLE = {The Evolution of Stramenopiles and Alveolates as Derived by ``Substitution Rate Calibration'' of Small Ribosomal Subunit {RNA}},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 42,
+ PAGES = {201-210},
+ PDF = {peer1996.jme.pdf},
+ DOI = {},
+ PMID = {8919872},
+ KEYWORDS = {small ribosomal subunit RNA; evolutionary distance; substitution rate calibration; stramenopiles; alveolates}
+ }
+
+ at ARTICLE{peer1997,
+ AUTHOR = {Van de Peer, Yves and Jansen, J. and De Rijk, P. and De Wachter, Rupert},
+ YEAR = 1997,
+ TITLE = {Database on the structure of small ribosomal subunit {RNA}},
+ JOURNAL = {Nucleic Acids Res.},
+ VOLUME = 25,
+ PAGES = {111-116},
+ PDF = {peer1997.nar.pdf},
+ DOI = {},
+ PMID = {9016516},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{peer2000,
+ AUTHOR = {Van de Peer, Yves and Baldauf, Sandra L. and Doolittle, W. Ford and Meyer, Axel},
+ YEAR = 2000,
+ TITLE = {An Updated and Comprehensive {rRNA} Phylogeny of (Crown) Eukaryotes Based on Rate-Calibrated Evolutionary Distances},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 51,
+ PAGES = {565-576},
+ PDF = {peer2000.jme.pdf},
+ DOI = {10.1007/s002390010120},
+ PMID = {11116330},
+ KEYWORDS = {SSU rRNA database; Among-site rate variation; Eukaryotic diversity; Crown eukaryotes; Distance trees; Rate variation among lineages}
+ }
+
+ at ARTICLE{peer2000a,
+ AUTHOR = {Van de Peer, Y. and De Rijk, P. and Wuyts, J. and Winkelmans, T. and De Wachter, R.},
+ TITLE = {The {E}uropean Small Subunit Ribosomal {RNA} Database},
+ JOURNAL = {Nucleic Acids Res.},
+ YEAR = 2000,
+ VOLUME = 28,
+ PAGES = {175-176},
+ PDF = {peer2000a.nar.pdf},
+ DOI = {},
+ PMID = {10592217},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{peer2001,
+ AUTHOR = {Van de Peer, Yves and Taylor, John S. and Braasch, Ingo and Meyer Axel},
+ YEAR = 2001,
+ TITLE = {The Ghost of Selection Past: Rates of Evolution and Functional Divergence of Anciently Duplicated Genes},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 53,
+ PAGES = {436-446},
+ PDF = {peer2001.jme.pdf},
+ DOI = {10.1007/s002390010233},
+ PMID = {11675603},
+ KEYWORDS = {Genome duplication; Functional divergence; Positive Darwinian selection; Relative rate test}
+ }
+
+ at MASTERSTHESIS{pelleg1998,
+ AUTHOR = {Pelleg, Dan},
+ YEAR = 1998,
+ TITLE = {Algorithms for Constructing Phylogenies from Quartets},
+ SCHOOL = {Israel Institute of Technology},
+ ADDRESS = {Haifa, Israel},
+ PDF = {pelleg1998.thesis.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Quartet methods; phylogeny}
+ }
+
+ at ARTICLE{pennisi2003,
+ AUTHOR = {Pennisi, Elisabeth},
+ YEAR = 2003,
+ TITLE = {Modernizing the Tree of Life},
+ JOURNAL = {Science},
+ VOLUME = 300,
+ PAGES = {1692-1697},
+ PDF = {pennisi2003.science.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Tree of Life; supertree},
+ REMARK = {See text boxes pennisi2003a, pennisi2003b}
+ }
+
+ at ARTICLE{pennisi2003a,
+ AUTHOR = {Pennisi, Elisabeth},
+ YEAR = 2003,
+ TITLE = {Drafting a Tree (Text Box)},
+ JOURNAL = {Science},
+ VOLUME = 300,
+ PAGES = {1694-1695},
+ PDF = {pennisi2003a.science.pdf pennisi2003.science.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Tree of Life; supertree}
+ }
+
+ at ARTICLE{pennisi2003b,
+ AUTHOR = {Pennisi, Elisabeth},
+ YEAR = 2003,
+ TITLE = {Plants Find Their Places on the Tree of Life (Text Box)},
+ JOURNAL = {Science},
+ VOLUME = 300,
+ PAGES = {1696},
+ PDF = {pennisi2003b.science.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Tree of Life; supertree; plants}
+ }
+
+ at ARTICLE{penny2001,
+ AUTHOR = {Penny, David and McComish, Bennet J. and Charleston, Michael A. and Hendy, Michael D.},
+ YEAR = 2001,
+ TITLE = {Mathematical Elegance with Biochemical Realism: The Covarion Model of Molecular Evolution},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 53,
+ PAGES = {711-723},
+ PDF = {penny2001.jme.pdf},
+ DOI = {10.1007/s002390010258},
+ PMID = {11677631},
+ KEYWORDS = {Covarion model; Hidden Markov; model Rates across sites Role of models in science}
+ }
+
+ at ARTICLE{peregrin2003,
+ AUTHOR = {Peregrin-Alvarez, Jos\'{e} Manuel and Tsoka, Sophia and Ouzounis, Christos A.},
+ YEAR = 2003,
+ TITLE = {The Phylogenetic Extent of Metabolic Enzymes and Pathways},
+ JOURNAL = {Genome Res.},
+ VOLUME = 13,
+ PAGES = {422-427},
+ PDF = {peregrin2003.genome-res.pdf},
+ DOI = {10.1101/gr.246903},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{perez2004,
+ AUTHOR = {P{\'e}rez-Losada, Marcos and H{\o}eg, Jens T. and Crandall, Keith A.},
+ YEAR = 2004,
+ TITLE = {Unraveling the Evolutionary Radiation of the {Thoracican} Barnacles Using Molecular and Morphological Evidence: A Comparison of Several Divergence Time Estimation Approaches},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 53,
+ PAGES = {244-264},
+ PDF = {perez2004.syst-biol.pdf},
+ DOI = {10.1080/10635150490423458},
+ PMID = {},
+ KEYWORDS = {divergence time estimation;; Calibration point; Cirripedia; divergence times; DNA sequences; fossils; genetic algorithms; mixed models; phylogeny}
+ }
+
+ at ARTICLE{perma1995,
+ AUTHOR = {Perma, Nicole T. and Kocher, Thomas D.},
+ YEAR = 1995,
+ TITLE = {Unequal Base Frequencies and the Estimation of Substitution Rates},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 12,
+ PAGES = {359-361},
+ PDF = {perma1995.mbe.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {mitochondrial DNA; substitution; composition}
+ }
+
+ at ARTICLE{perriere2000,
+ AUTHOR = {Perri\`{e}re, Guy and Duret, Laurent and Gouy, Manolo},
+ YEAR = 2000,
+ TITLE = {{HOBACGEN}: Database System for Comparative Genomics in Bacteria},
+ JOURNAL = {Genome Res.},
+ VOLUME = 10,
+ PAGES = {379-385},
+ PDF = {perriere2000.genome-res.pdf},
+ DOI = {},
+ PMID = {10720578},
+ KEYWORDS = {HOBACGEN; HOmologous BACterial GENes Database}
+ }
+
+ at ARTICLE{pesole1999,
+ AUTHOR = {Pesole, Graziano and Gissi, Carmela and De Chirico, Anna and Saccone, Cecilia},
+ YEAR = 1999,
+ TITLE = {Nucleotide Substitution Rate of Mammalian Mitochondrial Genomes},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 48,
+ PAGES = {427-434},
+ PDF = {pesole1999.jme.pdf},
+ DOI = {},
+ PMID = {10079281},
+ KEYWORDS = {Nucleotide substitution rate; Mammalia; Mitochondrial DNA; Comparative analysis}
+ }
+
+ at ARTICLE{pesole2000,
+ AUTHOR = {Pesole, Graziano and Gissi, Carmela and De Chirico, Anna and Saccone, Cecilia},
+ YEAR = 2000,
+ TITLE = {Lineage--Specific Evolutionary Rate in Mammalian {mtDNA}},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 17,
+ PAGES = {1022-1031},
+ PDF = {pesole2000.mbe.pdf},
+ DOI = {},
+ PMID = {10889215},
+ KEYWORDS = {mitochondrial DNA; mammalian phylogeny; molecular; evolution; nucleotide substitution rate; body size; metabolic rate; generation time}
+ }
+
+ at ARTICLE{pesole2001,
+ AUTHOR = {Pesole, Graziano and Saccone, Cecilia},
+ YEAR = 2001,
+ TITLE = {A Novel Method for Estimating Substitution Rate Variation Among Sites in a Large Dataset of Homologous DNA Sequences},
+ JOURNAL = {Genetics},
+ VOLUME = 157,
+ PAGES = {859-865},
+ PDF = {pesole2001.genetics.pdf},
+ DOI = {},
+ PMID = {11157002},
+ KEYWORDS = {}
+ }
+
+ at MASTERSTHESIS{petzold2003,
+ AUTHOR = {Petzold, Ekkehard},
+ YEAR = 2000,
+ TITLE = {Efficient Parameter Estimation for Maximum Likelihood Reconstruction of Phylogenetic Trees},
+ SCHOOL = {Universit\"at Leipzig},
+ ADRESS = {Leipzig, Germany},
+ TYPE = {Diplomarbeit},
+ PDF = {petzold2003.diplomathesis.pdf},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {parallel computing; parallel bioinformatics; Parameter Estimation; Maximum Likelihood; Phylogenetic Tree Reconstruction}
+ }
+
+ at ARTICLE{philippe1995,
+ AUTHOR = {Philippe, H. and Douzery, E.},
+ YEAR = 1995,
+ TITLE = {The pitfalls of molecular phylogeny based on four species as illustrated by the {Cetacea}/{Artiodactyla} relationships},
+ JOURNAL = {J. Mammalian Evol.},
+ VOLUME = 2,
+ PAGES = {133-152},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {quartet methods}
+ }
+
+ at ARTICLE{philippe1997,
+ AUTHOR = {Herv\'{e} Philippe},
+ YEAR = 1997,
+ TITLE = {Rodent Monophyly: Pitfalls of Molecular Phylogenies},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 45,
+ PAGES = {712-715},
+ PDF = {philippe1997.jme.pdf},
+ DOI = {},
+ PMID = {9419251},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{philippe1999,
+ AUTHOR = {Herv\'{e} Philippe and Forterre, Patrick},
+ YEAR = 1999,
+ TITLE = {The Rooting of the Universal Tree of Life Is Not Reliable},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 49,
+ PAGES = {509-523},
+ PDF = {philippe1999.jme.pdf},
+ DOI = {},
+ PMID = {10486008},
+ KEYWORDS = {Root of the tree of life; ATPase; Carbamoyl phosphate synthetase Elongation factor; tRNA synthetase; Signal recognition particle; Mutational saturation; Long branch attraction}
+ }
+
+ at ARTICLE{phillips1996,
+ AUTHOR = {Phillips, Cynthia A. and Warnow, Tandy J.},
+ YEAR = 1996,
+ TITLE = {The asymmetric median tree -- A new model for building consensus trees},
+ JOURNAL = {Discr. Appl. Math.},
+ VOLUME = 71,
+ PAGES = {311-335},
+ PDF = {phillips1996.discr-appl-math.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{phillips2003,
+ AUTHOR = {Phillips, Matthew J. and Penny, David},
+ YEAR = 2003,
+ TITLE = {The root of the mammalian tree inferred from whole mitochondrial genomes},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 28,
+ PAGES = {171-185},
+ PDF = {phillips2003.mpe.pdf},
+ DOI = {10.1016/S1055-7903(03)00057-5},
+ PMID = {},
+ KEYWORDS = {Marsupionta; Mitochondrial genomes; Monotremes; Partitioned likelihood; Pyrimidine bias; RY-coding; Theria;; mammalian tree; root; whole mitochondrial genomes}
+ }
+
+ at ARTICLE{phillips2004,
+ AUTHOR = {Phillips, Matthew J. and Delsuc, Fr{\'e}d{\'e}ric and Penny, David},
+ YEAR = 2004,
+ TITLE = {Genome-Scale Phylogeny and the Detection of Systematic Biases},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 21,
+ PAGES = {1455-1458},
+ PDF = {phillips2004.mbe.pdf,phillips2004.mbe-supplement.pdf},
+ REMARKS = {phillips2004.mbe-supplement1.pdf,phillips2004.mbe-supplement2.pdf,phillips2004.mbe-supplement3.pdf},
+ DOI = {10.1093/molbev/msh137},
+ PMID = {15084674},
+ KEYWORDS = {genome-scale phylogeny; systematic error; Saccharomyces; RY-coding}
+ }
+
+ at INCOLLECTION{piaggio2004,
+ AUTHOR = {Piaggio-Talice, Raul and Burleigh, Gordon and Eulenstein, Oliver},
+ TITLE = {Quartet Supertrees},
+ YEAR = 2004,
+ PAGES = {173-191},
+ EDITOR = {Bininda-Emonds, Olaf R. P.},
+ BOOKTITLE = {Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life},
+ PUBLISHER = {Kluwer Academic},
+ ADDRESS = {Dordrecht, The Netherlands},
+ PDF = {piaggio2004.supertrees.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertrees; quartets}
+ }
+
+ at ARTICLE{piau2002,
+ AUTHOR = {Piau, Didier},
+ YEAR = 2002,
+ TITLE = {Mutation-Replication Statistics of Polymerase Chain Reactions},
+ JOURNAL = {J. Comput. Biol.},
+ VOLUME = 9,
+ PAGES = {831-847},
+ PDF = {piau2002.jcb.pdf},
+ DOI = {10.1089/10665270260518308},
+ PMID = {},
+ KEYWORDS = {PCR errors; mutations; incomplete replications; mutation rates << 3/4}
+ }
+
+ at ARTICLE{piccolboni2003,
+ AUTHOR = {Piccolboni, Antonio and Gusfield, Dan},
+ YEAR = 2003,
+ TITLE = {On the Complexity of Fundamental Computational Problems in Pedigree Analysis},
+ JOURNAL = {J. Comput. Biol.},
+ VOLUME = 10,
+ PAGES = {763-773},
+ PDF = {piccolboni2003.jcb.pdf},
+ DOI = {10.1089/106652703322539088},
+ PMID = {},
+ KEYWORDS = {linkage analysis; computational complexity; pedigree}
+ }
+
+ at ARTICLE{piel2003,
+ AUTHOR = {Piel, William H. and Sanderson, Michael J. and Donoghue, Michael J.},
+ YEAR = 2003,
+ TITLE = {The small-world dynamics of tree networks and data mining in phyloinformatics},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 19,
+ PAGES = {1162-1168},
+ PDF = {piel2003.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg131},
+ PMID = {12801879},
+ KEYWORDS = {small-world dynamics; tree networks; data mining; TreeBASE}
+ }
+
+ at ARTICLE{pinou1996,
+ AUTHOR = {Pinou, Theodora and Schlick, Tamar and Li, Bin and Dowling, H. G.},
+ YEAR = 1996,
+ TITLE = {Addition of Darwin's Third Dimension to Phyletic Trees},
+ JOURNAL = {J. theor. Biol.},
+ VOLUME = 182,
+ PAGES = {505-512},
+ PDF = {pinou1996.jtb.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {3D visualizing; visualizing phyletic relationship}
+ }
+
+ at ARTICLE{piontkivska2004,
+ AUTHOR = {Piontkivska, Helen},
+ YEAR = 2004,
+ TITLE = {Efficiencies of maximum likelihood methods of phylogenetic inferences when different substitution models are used},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 31,
+ PAGES = {865-873},
+ PDF = {piontkivska2004.mpe.pdf},
+ DOI = {10.1016/j.ympev.2003.10.011},
+ PMID = {},
+ KEYWORDS = {ML; PAUP*; Maximum likelihood; Nucleotide substitution model; Phylogenetic tree; Topological distance}
+ }
+
+ at ARTICLE{pisani2002,
+ AUTHOR = {Pisani, Davide and Wilkinson, Mark},
+ YEAR = 2002,
+ TITLE = {Matrix Representation with Parsimony, Taxonomic Congruence, and Total Evidence},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 51,
+ PAGES = {151-155},
+ PDF = {pisani2002.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertrees; Matrix Representation with Parsimony, MRP; Taxonomic Congruence; Total Evidence}
+ }
+
+ at ARTICLE{pisanti2003,
+ AUTHOR = {Pisanti, N. and Marangoni, R. and Ferragina, P. and Frangioni, A. and Savona, A. and Pisanelli, C. and Luccio, F.},
+ YEAR = 2003,
+ TITLE = {{PaTre}: A Method for Paralogy Trees Construction},
+ JOURNAL = {J. Comput. Biol.},
+ VOLUME = 10,
+ PAGES = {791-802},
+ PDF = {pisanti2003.jcb.pdf},
+ DOI = {10.1089/106652703322539105},
+ PMID = {},
+ KEYWORDS = {gene families; paralog genes; paralogy trees; transformation distance; lightest spanning arborescence; duplications}
+ }
+
+ at ARTICLE{pitman2001,
+ AUTHOR = {Pitman, Jim},
+ YEAR = 2001,
+ TITLE = {Random Mappings, Forests, and Subsets Associated with {Abel}-{Cayley}-{Hurwitz} Multinomial Expansions},
+ JOURNAL = {SLC},
+ VOLUME = 46,
+ PAGES = {h},
+ PDF = {pitman2001.slc.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{plastino2003,
+ AUTHOR = {Plastino, A. and Ribeiro, C. C. and Rodriguez, N.},
+ YEAR = 2003,
+ TITLE = {Developing {SPMD} applications with load balancing},
+ JOURNAL = {Parallel Comput.},
+ VOLUME = 29,
+ PAGES = {743-766},
+ PDF = {plastino2003.parallel-comput.pdf},
+ DOI = {10.1016/S0167-8191(03)00060-7},
+ PMID = {},
+ KEYWORDS = {scheduling; parallel computing; Load balancing; SPMD; Frameworks; Data parallelism; Parallel algorithms}
+ }
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+ at TECHREPORT{plata1994,
+ AUTHOR = {Plata, Oscar and Rivera, Francisco F.},
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+ NUMBER = {UMA-DAC-94/09},
+ INSTITUTION = {University of Malaga, Department of Computer Architecture},
+ ADDRESS = {Malaga, Spain},
+ PDF = {plata1994.UMA-DAC-94-09.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel computing; static scheduling; dynamic scheduling; load balancing}
+ }
+
+ at INPROCEEDINGS{plata1994a,
+ AUTHOR = {Plata, Oscar and Rivera, Francisco F.},
+ YEAR = 1994,
+ TITLE = {Combining Static and Dynamic Scheduling an Distributed-Memory Multiprocessors},
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+ at ARTICLE{plyusnin2002a,
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+ }
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+ PMID = {},
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+ }
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+ DOI = {10.1006/mpev.2001.1074},
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+ PAGES = {2010-2018},
+ PDF = {rodrigo2003.mbe.pdf},
+ DOI = {10.1093/molbev/msg215},
+ PMID = {12949147},
+ KEYWORDS = {serial samples; substitution rate; subtree likelihood; whole-tree likelihood; maximum likelihood}
+ }
+
+ at ARTICLE{rodriguez1990,
+ AUTHOR = {Rodriguez, F. and Oliver, J. L. and Main, A. and Medina, J. R.},
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+ }
+
+ at ARTICLE{rodriguez1998,
+ AUTHOR = {Rodriguez, Luis L. and Owens, Jessica H. and Peters, Clarence J. and Nichol, Stuart T.},
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+ PDF = {rodriguez1998.virology.pdf},
+ DOI = {},
+ PMID = {},
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+ }
+
+ at TECHREPORT{rodriguez1998a,
+ AUTHOR = {Rodriguez, A. and de la Fraga, L. G. and Zapata, E. L. and Carazo, J. M. and Trelles, O.},
+ YEAR = 1998,
+ TITLE = {Biological Sequence Analysis on Distributed-Shared Memory Multiprocessors},
+ TYPE = {Technical Report},
+ NUMBER = {UMA-DAC-98/33},
+ INSTITUTION = {University of Malaga, Department of Computer Architecture},
+ ADDRESS = {Malaga, Spain},
+ PDF = {rodriguez1998a.UMA-DAC-98-33.pdf},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {parallel bioinformatics; parallel computing; Biological Sequence Analysis}
+ }
+
+ at INPROCEEDINGS{rodriguez1998b,
+ AUTHOR = {Rodriguez, A. and de la Fraga, L. G. and Zapata, E. L. and Carazo, J. M. and Trelles, O.},
+ YEAR = 1998,
+ TITLE = {Biological Sequence Analysis on Distributed-Shared Memory Multiprocessors},
+ BOOKTITLE = {Proceedings of the 6th Euromicro WorkShop on Parallel and Distributed Processing (PDP'98)},
+ ADRESS = {Madrid, Spain},
+ REMARKS = {Techreport: rodriguez1998a.UMA-DAC-98-33.pdf; rodriguez1998a},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {parallel bioinformatics; parallel computing; Biological Sequence Analysis}
+ }
+
+ at TECHREPORT{rodriguez2000,
+ AUTHOR = {Rodriguez, A. and Perez-Pulido, A. and Lopez, A. D. and Thode, G. and Carazo, J. M. and Trelles, O.},
+ YEAR = 2000,
+ TITLE = {Mining Low-level Similarity Signals from Sequence Databases},
+ TYPE = {Technical Report},
+ NUMBER = {UMA-DAC-00/25},
+ INSTITUTION = {University of Malaga, Department of Computer Architecture},
+ ADDRESS = {Malaga, Spain},
+ PDF = {rodriguez2000.UMA-DAC-00-25.pdf},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {parallel bioinformatics; parallel computing; Similarity search; Sequence Databases}
+ }
+
+ at INPROCEEDINGS{rodriguez2000a,
+ AUTHOR = {Rodriguez, A. and Perez-Pulido, A. and Lopez, A. D. and Thode, G. and Carazo, J. M. and Trelles, O.},
+ YEAR = 2000,
+ TITLE = {Mining Low-level Similarity Signals from Sequence Databases},
+ BOOKTITLE = {Proceedings of the 4th World Multiconference on systematics, Cybernetics, and Informatics (SCI 2000) / the 6th International Conference on Information Systems, Analysis and Synthesis (ISAS 2000)},
+ ADRESS = {Orlando, Florida, USA},
+ MONTH = {July},
+ REMARKS = {Techreport: rodriguez2000.UMA-DAC-00-25.pdf; rodriguez2000},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {parallel bioinformatics; parallel computing; Similarity search; Sequence Databases}
+ }
+
+ at ARTICLE{roeser2001,
+ AUTHOR = {R{\"o}ser, Martin and Winterfeld, Grit and Grebenstein, B{\"a}rbel and Hemleben, Vera},
+ YEAR = 2001,
+ TITLE = {Molecular Diversity and Physical Mapping of {5S} {rDNA} in Wild and Cultivated Oat Grasses ({Poaceae}: {Aveneae})},
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+ PAGES = {198-217},
+ PDF = {roeser2001.mpe.pdf},
+ DOI = {10.1006/mpev.2001.1003},
+ PMID = {11697916},
+ KEYWORDS = {Poaceae; Aveneae; Avena; Helictotrichon; Pseudarrhenatherum; Lagurus; Trisetum; 5S rDNA; transcription; pseudogene; polyploidy; DNA in situ hybridization; FISH}
+ }
+
+ at ARTICLE{rogers1998,
+ AUTHOR = {Rogers, James S. and Swofford, David L.},
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+ KEYWORDS = {Approximations; maximum likelihood; parsimony; tree searching}
+ }
+
+ at ARTICLE{rogers1999,
+ AUTHOR = {Rogers, James S. and Swofford, David L.},
+ YEAR = 1999,
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+ PDF = {rogers1999.mbe.pdf},
+ DOI = {},
+ PMID = {10507922},
+ KEYWORDS = {phylogenetic trees; maximum likelihood; multiple local maxima; simulations; nucleotide sequences}
+ }
+
+ at ARTICLE{rogers2001,
+ AUTHOR = {Rogers, James S.},
+ YEAR = 2001,
+ TITLE = {Maximum Likelihood Estimation of Phylogenetic Trees Is Consistent When Substitution Rates Vary According to the Invariable Sites plus Gamma Distribution},
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+ PDF = {rogers2001.syst-biol.pdf},
+ DOI = {},
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+ KEYWORDS = {consistency; general time reversible model; maximum likelihood; phylogeny estimation; rate heterogeneity}
+ }
+
+ at PHDTHESIS{rognes2000a,
+ AUTHOR = {Rognes, Torbj\orn},
+ YEAR = 2000,
+ TITLE = {Rapid and sensitive methods for protein sequence comparison and database searching},
+ SCHOOL = {Institute of Medical Microbiology, University of Oslo},
+ ADRESS = {Norway},
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+ MONTH = {July},
+ ISBN = {82-7633-154-8},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{rognes2000,
+ AUTHOR = {Rognes, Torbj\orn and Seeberg, Erling},
+ YEAR = 2000,
+ TITLE = {Six-fold speed-up of {Smith-Waterman} sequence database searches using parallel processing on common microprocessors},
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+ PDF = {rognes2000.bioinformatics.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing; Intel Pentium Processors; MMX; SSE; micro parallelism; Smith-Waterman}
+ }
+
+ at ARTICLE{rognes2001,
+ AUTHOR = {Rognes, Torbj\orn},
+ YEAR = 2001,
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+ KEYWORDS = {parallel bioinformatics; parallel computing; Smith-Waterman; alignment}
+ }
+
+ at ARTICLE{rokas2001,
+ AUTHOR = {Rokas, Antonis},
+ YEAR = 2001,
+ TITLE = {Getting it right for the wrong reason},
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+ PAGES = {668},
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+ PMID = {},
+ KEYWORDS = {Felsenstein zone; phylogenetic bias; maximum likelihood; parsimony; phylogenetics; UPGMA}
+ }
+
+ at ARTICLE{rokas2002,
+ AUTHOR = {Rokas, Antonis and Nylander, Johan A. A. and Ronquist, Fredrik and Stone, Graham N.},
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+ DOI = {10.1006/mpev.2001.1032},
+ PMID = {11820842},
+ KEYWORDS = {gallwasps; Cynipidae; Hymenoptera; likelihood; DNA sequence; rDNA; EF1a F1; opsin; cytochrome b; cytochrome oxidase I; insect systematics.}
+ }
+
+ at ARTICLE{rokas2003,
+ AUTHOR = {Rokas, Antonis and Ladoukakis, Emmanuel and Zouros, Eleftherios},
+ YEAR = 2003,
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+ DOI = {10.1016/S0169-5347(03)00125-3},
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+ KEYWORDS = {mitochondrial DNA recombination}
+ }
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+ at ARTICLE{ronquist2003,
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+ }
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+ at ARTICLE{rosenberg2001,
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+ YEAR = 2001,
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+ TITLE = {Heterogeneity of Nucleotide Frequencies Among Evolutionary Lineages and Phylogenetic Inference},
+ JOURNAL = {Mol. Biol. Evol.},
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+ PDF = {rosenberg2003.mbe.pdf},
+ DOI = {10.1093/molbev/msg067},
+ PMID = {12679548},
+ KEYWORDS = {LogDet distances; nonstationarity; heterogeneous nucleotide composition; phylogenetic inference; taxon sampling}
+ }
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+ at ARTICLE{rosenberg2003a,
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+ INSTITUTION = {University New Mexico},
+ ADDRESS = {Albuquerque, NM, USA},
+ TYPE = {UNM Computer Science Tech-Reports},
+ NUMBER = {TR-CS-2003-32},
+ PDF = {roshan2003.TR-CS-2003-32.ps.gz},
+ KEYWORDS = {DCM; Iterative-DCM3; Large Phylogenetic Trees}
+ }
+
+ at INCOLLECTION{roshan2004,
+ AUTHOR = {Roshan, Usman and Moret, Bernard M. E. and Williams, Tiffani L. and Warnow, Tandy},
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+ YEAR = 2004,
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+ EDITOR = {Bininda-Emonds, Olaf R. P.},
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+ PUBLISHER = {Kluwer Academic},
+ ADDRESS = {Dordrecht, The Netherlands},
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+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertrees; DCM; Performance}
+ }
+
+ at TECHREPORT{roshan2004a,
+ AUTHOR = {Roshan, Usman and Moret, Bernard M. E. and Williams, Tiffani L. and Warnow, Tandy},
+ YEAR = 2004,
+ TITLE = {Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees},
+ INSTITUTION = {University New Mexico},
+ ADDRESS = {Albuquerque, NM, USA},
+ TYPE = {UNM Computer Science Tech-Reports},
+ NUMBER = {TR-CS-2004-07},
+ PDF = {roshan2004a.TR-CS-2004-07.pdf},
+ KEYWORDS = {DCM; Rec-I-DCM3; Large Phylogenetic Trees}
+ }
+
+ at ARTICLE{rosinski1999,
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+ }
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+ }
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+ at ARTICLE{ruvolo1996,
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+
+ at ARTICLE{rzhetsky1993,
+ AUTHOR = {Rzhetsky, Andrey and Nei, Masatoshi},
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+
+ at ARTICLE{rzhetsky1995,
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+ at ARTICLE{rzhetsky1996,
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+ AUTHOR = {Saitou, Naruya},
+ YEAR = 2002,
+ TITLE = {Evolutionary genomics: Molecular evolution at the genomic scale},
+ JOURNAL = {Trends Genet.},
+ VOLUME = 18,
+ PAGES = {239-240},
+ PDF = {saitou2002.tig.pdf},
+ DOI = {10.1016/S0168-9525(02)02675-6},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{sakakibara2003,
+ AUTHOR = {Sakakibara, Yasubumi},
+ YEAR = 2003,
+ TITLE = {Pair hidden {Markov} models on tree structures},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 19,
+ PAGES = {i232-i240},
+ PDF = {sakakibara2003.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg1032},
+ PMID = {12855464},
+ KEYWORDS = {Pair hidden Markov models; pair HMMs; tree structures}
+ }
+
+ at ARTICLE{salamin2003,
+ AUTHOR = {Salamin, Nicolas and Chase, Mark W. and Hodkinson, Trevor R. and Savolainen, Vincent},
+ YEAR = 2003,
+ TITLE = {Assessing internal support with large phylogenetic {DNA} matrices},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 27,
+ PAGES = {528-539},
+ PDF = {salamin2003.mpe.pdf},
+ DOI = {10.1016/S1055-7903(03)00011-3},
+ PMID = {},
+ KEYWORDS = {large phylogenetic DNA matrices; internal support}
+ }
+
+ at ARTICLE{salamin2002,
+ AUTHOR = {Salamin, Nicolas and Hodkinson, Trevor R. and Savolainen, Vincent},
+ YEAR = 2002,
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+ VOLUME = 51,
+ PAGES = {136-150},
+ PDF = {salamin2002.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Matrix representation with parsimony; phylogeny; Poaceae; supertree}
+ }
+
+ at ARTICLE{salceda2004,
+ AUTHOR = {Salceda, Jes{\'u}s and D{\'i}az, Iv{\'a}n and Touri{\~n}io, Juan and Doallo, Ram{\'o}n},
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+ PAGES = {759-766},
+ PDF = {salceda2004.jpdc.pdf},
+ DOI = {10.1016/j.jpdc.2003.10.009},
+ PMID = {},
+ KEYWORDS = {parallel computing; grid computing; middleware;; Middleware; Management; Distributed systems; CIM; LDAP; Distributed Management Task Force (DMTF)}
+ }
+
+ at ARTICLE{salemi1998,
+ AUTHOR = {Salemi, Marco and Vandamme, Anne-Mieke and Gradozzi, Chiara and Van Laethem, Kristel and Cattaneo, Ercole and Taylor, Graham and Casoli, Claudio and Goubau, Patrick and Desmyter, Jan and Bertazzoni, Umberto},
+ YEAR = 1998,
+ TITLE = {Evolutionary Rate and Genetic Heterogeneity of Human {T}-Cell Lymphotropic Virus Type {II} {(HTLV-II)} Using Isolates from European Injecting Drug Users},
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+ VOLUME = 46,
+ PAGES = {602-611},
+ PDF = {salemi1998.jme.pdf},
+ DOI = {},
+ PMID = {9545470},
+ KEYWORDS = {HTLV-II, IIa and IIb subtypes; Restriction analysis; Phylogenetic analysis; Maximum likelihood; Neighbour-joining; Parsimony; Molecular clock; Fixation rate}
+ }
+
+ at ARTICLE{salemi2002,
+ AUTHOR = {Salemi, Marco and Vandamme, Anne-Mieke},
+ YEAR = 2002,
+ TITLE = {Hepatitis {C} Virus Evolutionary Patterns Studied Through Analysis of Full-Genome Sequences},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 54,
+ PAGES = {62-70},
+ PDF = {salemi2002.jme.pdf},
+ DOI = {},
+ PMID = {11734899},
+ KEYWORDS = {Hepatitis C virus; Evolutionary models; Star-like phylogeny; Likelihood ratio test; Gamma distribution; Molecular clock}
+ }
+
+ at BOOK{salemi2003,
+ EDITOR = {Salemi, Marco and Vandamme, Anne-Mieke},
+ YEAR = 2003,
+ TITLE = {The Phylogenetic Handbook: A Practical Approach to {DNA} and Protein Phylogeny},
+ PUBLISHER = {Cambridge University Press},
+ ADDRESS = {Cambridge, UK},
+ ISBN = {052180390X },
+ KEYWORDS = {},
+ NOTE = {to appear}
+ }
+
+ at ARTICLE{salemi2003a,
+ AUTHOR = {Salemi, Marco and De Oliveira, Tulio and Courgnaud, Valerie and Moulton, Vincent and Holland, Barbara and Cassol, Sharon and Switzer, William M. and Vandamme, Anne-Mieke},
+ YEAR = 2003,
+ TITLE = {Mosaic Genomes of the Six Major Primate Lentivirus Lineages Revealed by Phylogenetic Analyses},
+ JOURNAL = {J. Virol.},
+ VOLUME = 77,
+ PAGES = {7202-7213},
+ PDF = {salemi2003a.j-virol.pdf},
+ DOI = {10.1128/JVI.77.13.7202-7213.2003},
+ PMID = {12805419},
+ KEYWORDS = {Mosaic Genomes; Primate Lentivirus; Phylogenetic Analysis}
+ }
+
+ at ARTICLE{salisbury1999,
+ AUTHOR = {Salisbury, Benjamin A.},
+ YEAR = 1999,
+ TITLE = {Strongest Evidence: Maximum Apparent Phylogenetic Signal as a New Cladistic Optimality Criterion},
+ JOURNAL = {Cladistics},
+ VOLUME = 15,
+ PAGES = {137-149},
+ PDF = {salisbury1999.cladistics.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
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+ at ARTICLE{salisbury1999a,
+ AUTHOR = {Salisbury, Benjamin A.},
+ YEAR = 1999,
+ TITLE = {Strongest evidence in compatibility: Clique and tree evaluation using apparent phylogenetic signal},
+ JOURNAL = {Taxon},
+ VOLUME = 48,
+ PAGES = {755-766},
+ KEYWORDS = {compatibility; clique evaluation; tree evaluation; phylogenetic signal},
+ PDF = {hardcopy},
+ DOI = {},
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+ KEYWORDS = {}
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+
+ at ARTICLE{salisbury2001,
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+ VOLUME = 50,
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+ }
+
+ at INCOLLECTION{salminen1995,
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+ AUTHOR = {Salminen, Mika O. and Carr, Jean K. and Burke, Donald S. and McCutchan, Francine E.},
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+ at ARTICLE{salter2001,
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+ VOLUME = 50,
+ PAGES = {7-17},
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+ at ARTICLE{salter2001a,
+ AUTHOR = {Salter, Laura A.},
+ YEAR = 2001,
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+ KEYWORDS = {Adaptive radiation; Cichlidae; Lake Tanganyika; mitochondrial DNA sequences; molecular phylogeny; species flock}
+ }
+
+ at ARTICLE{sammeth2003,
+ AUTHOR = {Sammeth, M. and Rothg{\"a}nger, J. and Esser, W. and Albert, J. and Stoye, J. and Harmsen, D.},
+ YEAR = 2003,
+ TITLE = {{QAlign}: quality-based multiple alignments with dynamic phylogenetic analysis},
+ JOURNAL = {Bioinformatics},
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+ PDF = {sammeth2003.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg197},
+ PMID = {12912847},
+ KEYWORDS = {Multiple sequence aligment; GUI; clustalw; t-coffee; DCA; dialign}
+ }
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+ at ARTICLE{sammeth2003a,
+ AUTHOR = {Sammeth, Michael and Morgenstern, Burkhard and Stoye, Jens},
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+ JOURNAL = {Bioinformatics},
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+ PAGES = {ii189-ii195},
+ PDF = {sammeth2003a.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg1077},
+ PMID = {12912847},
+ KEYWORDS = {Multiple sequence aligment; divide-and-conquer alignment}
+ }
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+ at INPROCEEDINGS{sancese1999,
+ AUTHOR = {Sancese, S. and Ciancarini, P. and Messina, A.},
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+ PAGES = {320-334},
+ PUBLISHER = {Springer},
+ ADDRESS = {New York},
+ PDF = {sancese1999.LNCS.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel computing; Message Passing; Tuple Space Coordination; Aerodynamics Application}
+ }
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+ AUTHOR = {Sanderson, Michael J.},
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+ PMID = {},
+ KEYWORDS = {phylogenies; trees; bootstrap; Confidence limits; "confidence intervals" on trees; majority rule consensus; median consensus tree}
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+
+ at ARTICLE{sanderson1998,
+ AUTHOR = {Sanderson, Michael J. and Purvis, Andy and Henze, Chris},
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+ at ARTICLE{sanderson2002,
+ AUTHOR = {Sanderson, Michael J.},
+ YEAR = 2002,
+ TITLE = {Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach},
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+ PDF = {sanderson2002.mbe.pdf},
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+ at ARTICLE{sanderson2002a,
+ AUTHOR = {Sanderson, Michael J. and Shaffer, H. Bradley},
+ YEAR = 2002,
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+ at ARTICLE{sanderson2003,
+ AUTHOR = {Sanderson, Michael J.},
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+ at ARTICLE{sanderson2003a,
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+ DOI = {10.1093/molbev/msg115},
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+ at INPROCEEDINGS{sankoff1998a,
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+ TITLE = {Phylogeny, fossils, and model systems in the study of evolutionary developmental biology},
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+ PAGES = {379-383},
+ PDF = {santini2002.mpe.pdf},
+ DOI = {10.1016/S1055-7903(02)00209-9},
+ PMID = {},
+ KEYWORDS = {Phylogeny; Fossils; Tetraodontiformes; Hox genes; Model organisms; Evolutionary developmental biology}
+ }
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+ at ARTICLE{santos2004,
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+ DOI = {10.1016/j.tig.2003.12.009},
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+ }
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+ at ARTICLE{sars2004,
+ AUTHOR = {{The Chinese {SARS} Molecular Epidemiology Consortium}},
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+ DOI = {10.1126/science.1092002},
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+ at ARTICLE{sato2001,
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+ at ARTICLE{schadt2002a,
+ AUTHOR = {Schadt, Eric and Sinsheimer, Janet S. and Lange, Kenneth},
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+ AUTHOR = {Schierup, Mikkel H. and Hein, Jotun},
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+ PAGES = {879-891},
+ PDF = {schierup2000a.genetics.pdf},
+ DOI = {},
+ PMID = {11014833},
+ KEYWORDS = {}
+ }
+
+ at BOOK{schierwater1994,
+ EDITOR = {Schierwater, B. and Streit, B. and DeSalle, R. and Wagner, G. P.},
+ YEAR = 1994,
+ TITLE = {Molecular Ecology and Evolution - Approaches and Applications},
+ SERIES = {Experientia Supplementum (EXS)},
+ VOLUME = 69,
+ PUBLISHER = {Birkhauser},
+ ADDRESS = {Boston}
+ }
+
+ at ARTICLE{schimmel1998,
+ AUTHOR = {Schimmel, Paul and Alexander, Rebecca},
+ YEAR = 1998,
+ TITLE = {All You Need Is {RNA}},
+ JOURNAL = {Science},
+ VOLUME = 281,
+ PAGES = {658-659},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {9714675},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{schlaepfer2002,
+ AUTHOR = {Schlaepfer, Martin A. and Runge, Michael C. and Sherman, Paul W.},
+ YEAR = 2002,
+ TITLE = {Ecological and evolutionary traps},
+ JOURNAL = {TREE},
+ VOLUME = 17,
+ PAGES = {474-480},
+ PDF = {schlaepfer2002.tree.pdf},
+ DOI = {10.1016/S0169-5347(02)02580-6},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{schloesser1984,
+ AUTHOR = {Schl{\"o}sser, U. G.},
+ YEAR = 1984,
+ TITLE = {{Sammlung} von {Algenkulturen}: {Additions} to the collection since 1982},
+ JOURNAL = {Ber. Deutsch. Bot. Ges.},
+ VOLUME = 97,
+ PAGES = {465-475},
+ PDF = {NICHT VORHANDEN},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{schloetterer2003,
+ AUTHOR = {Schl{\"o}tterer, Christian},
+ YEAR = 2003,
+ TITLE = {Hitchhiking mapping ? functional genomics from the population genetics perspective},
+ JOURNAL = {Trends Genet.},
+ VOLUME = 19,
+ PAGES = {32-38},
+ PDF = {schloetterer2003.tig.pdf},
+ DOI = {10.1016/S0168-9525(02)00012-4},
+ PMID = {},
+ KEYWORDS = {statistical tests; population genetic theory; beneficial mutations; multilocus approach; positive selection; hitchhiking mapping}
+ }
+
+ at ARTICLE{schlosshauer2002,
+ AUTHOR = {Schlosshauer, Maximilian and Ohlsson, Mattias},
+ YEAR = 2002,
+ TITLE = {A novel approach to local reliability of sequence alignments},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 18,
+ PAGES = {847-854},
+ PDF = {schlosshauer2002.bioinformatics.pdf},
+ DOI = {},
+ PMID = {12075020},
+ KEYWORDS = {}
+ }
+
+ at MASTERSTHESIS{schmidt1996,
+ AUTHOR = {Schmidt, Heiko A.},
+ TITLE = {{Parallelisierung} phylogenetischer {Methoden} zur {Untersuchung} der {Crown}-{Group}-{Radiation}},
+ YEAR = 1996,
+ SCHOOL = {Universit{\"a}t zu K{\"o}ln},
+ TYPE = {Diplomarbeit},
+ PDF = {schmidt1996.diplom.pdf},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {parallel bioinformatics; parallel computing; phylogeny reconstruction; pfastDNAml; DNAml; Crown Group Radiation; mtDNA}
+ }
+
+ at ARTICLE{schmidt2002,
+ AUTHOR = {Schmidt, Heiko A. and Strimmer, Korbinian and Vingron, Martin and von Haeseler, Arndt},
+ YEAR = 2002,
+ TITLE = {{TREE-PUZZLE}: Maximum likelihood phylogenetic analysis using quartets and parallel computing},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 18,
+ PAGES = {502-504},
+ PDF = {schmidt2002.bioinformatics.pdf},
+ DOI = {},
+ PMID = {11934758},
+ KEYWORDS = {parallel bioinformatics; parallel computing; TREE-PUZZLE; quartet puzzling; phylogeny reconstruction}
+ }
+
+ at INCOLLECTION{schmidt2002a,
+ AUTHOR = {Schmidt, Heiko A. and von Haeseler, Arndt},
+ YEAR = 2002,
+ TITLE = {Quartet Trees as a Tool to Reconstruct Large Trees from Sequences},
+ PAGES = {379-388},
+ EDITOR = {Jajuga, Krzysztof and Soko{\l}owski, Andrzej and Bock, Hans-Hermann},
+ BOOKTITLE = {Data Analysis, Classification, and Related Methods},
+ SERIES = {Studies in Classification, Data Analysis, and Knowledge Organization},
+ PUBLISHER = {Springer},
+ ADDRESS = {Heidelberg, New York},
+ ISBN = {3-540-43691-X},
+ PDF = {schmidt2002b.IFCS2002-manuscr.pdf},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {large phylogeny analysis; decomposition and assembly of large datasets; quartet puzzling}
+ }
+
+ at INPROCEEDINGS{schmidt2002b,
+ AUTHOR = {Schmidt, Heiko A. and von Haeseler, Arndt},
+ YEAR = 2002,
+ TITLE = {Quartet Trees as a Tool to Reconstruct Large Trees from Sequences},
+ PAGES = {379-388},
+ BOOKTITLE = {Proceedings of the 9th Conference of the International Federation of Classification Societies (IFCS-2002)},
+ MONTH = {November},
+ PUBLISHER = {Springer},
+ ADDRESS = {Heidelberg, New York},
+ PDF = {schmidt2002b.IFCS2002-manuscr.pdf},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {large phylogeny analysis; decomposition and assembly of large datasets; quartet puzzling}
+ }
+
+ at INCOLLECTION{schmidt2003,
+ AUTHOR = {Schmidt, Heiko A. and von Haeseler, Arndt},
+ TITLE = {Maximum Likelihood Analysis Using {TREE-PUZZLE}},
+ YEAR = 2003,
+ PAGES = {6.6.1-6.6.25},
+ EDITOR = {Baxevanis, Andreas D. and Davison, Daniel B. and Page, Roderic D. M. and Stormo, Gary and Stein, Lincoln},
+ BOOKTITLE = {Current Protocols in Bioinformatics},
+ PUBLISHER = {Wiley and Sons},
+ ADDRESS = {New York, USA},
+ PDF = {schmidt2002c.cpbi-66-manuscript.pdf, schmidt2002c.cpbi-66-figures.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Quartet Puzzling, Likelihood Mapping, Maximum Likelihood, Phylogeny, Evolution, Tree Comparison}
+ }
+
+ at ARTICLE{schmidt2003a,
+ AUTHOR = {Schmidt, H. A. and Petzold, E. and Vingron, M. and von Haeseler, A.},
+ YEAR = 2003,
+ TITLE = {Molecular Phylogenetics: Parallelized Parameter Estimation and Quartet Puzzling},
+ JOURNAL = {J. Parallel Distrib. Comput.},
+ VOLUME = 63,
+ PAGES = {719-727},
+ PDF = {schmidt2003a.jpdc-manuscript.pdf},
+ DOI = {10.1016/S0743-7315(03)00129-1},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing;; phylogeny reconstruction, quartet puzzling algorithm, parameter estimation, TREE-PUZZLE, message passing, scheduling algorithms}
+ }
+
+ at PHDTHESIS{schmidt2003b,
+ AUTHOR = {Schmidt, Heiko A.},
+ TITLE = {Phylogenetic Trees from Large Datasets},
+ YEAR = 2003,
+ SCHOOL = {Universit{\"a}t D{\"u}sseldorf},
+ PDF = {schmidt2003b.phdthesis.pdf},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {parallel bioinformatics; parallel computing; phylogeny reconstruction; quartet puzzling}
+ }
+
+ at ARTICLE{schneider1990,
+ AUTHOR = {Schneider, Thomas D. and Stephens, R. Michael},
+ YEAR = 1990,
+ TITLE = {Sequence logos: A new way to display consensus sequences},
+ JOURNAL = {Nucleic Acids Res.},
+ VOLUME = 18,
+ PAGES = {6097-6100},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {information theory; sequence logos}
+ }
+
+ at BOOK{schneider1991,
+ EDITOR = {Schneider, Hans--Jochen},
+ YEAR = 1991,
+ TITLE = {{L}exikon der {I}nformatik und {D}atenverarbeitung},
+ PUBLISHER = {Oldenbourg Verlag},
+ ADDRESS = {M{\"u}nchen}
+ }
+
+ at UNPUBLISHED{schneider1996,
+ AUTHOR = {Schneider, Thomas D. and Stephens, R. Michael},
+ YEAR = 1996,
+ MONTH = {February},
+ TITLE = {Sequence Logos: A New Way to Display Consensus Sequences},
+ NOTE = {Update of \emph{Nucleic Acids Res.}, 18:6097-6100, 1990},
+ PDF = {schneider1996.mimeo.ps},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {information theory; sequence logo}
+ }
+
+ at ARTICLE{schneider1997,
+ AUTHOR = {Schneider, Thomas D.},
+ YEAR = 1997,
+ TITLE = {Sequence walkers: A graphical method to display how binding proteins interact with {DNA} or {RNA} sequences},
+ JOURNAL = {Nucleic Acids Res.},
+ VOLUME = 25,
+ PAGES = {4408-4415},
+ PDF = {schneider1997.nar.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {information theory; sequence logo; walker}
+ }
+
+ at ARTICLE{schneider1997a,
+ AUTHOR = {Schneider, Thomas D.},
+ YEAR = 1997,
+ TITLE = {Information Content of Individual Genetic Sequences},
+ JOURNAL = {J. theor. Biol.},
+ VOLUME = 189,
+ PAGES = {427-441},
+ PDF = {schneider1997a.j-theor-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {information theory; sequence logo; walker}
+ }
+
+ at UNPUBLISHED{schneider1999,
+ AUTHOR = {Schneider, Thomas D.},
+ YEAR = 1999,
+ MONTH = {December},
+ TITLE = {Information Content of Individual Genetic Sequences},
+ NOTE = {Update of \emph{J. Theor. Biol.}, 189:427-441, 1997, with an appendix by John Spouge},
+ PDF = {schneider1999.mimeo.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {DNA-protein interaction; information theory; sequence logo; walker}
+ }
+
+ at ARTICLE{schneider2000,
+ AUTHOR = {Schneider, Thomas D.},
+ YEAR = 2000,
+ TITLE = {Evolution of biological information},
+ JOURNAL = {Nucleic Acids Res.},
+ VOLUME = 28,
+ PAGES = {2794-2799},
+ PDF = {schneider2000.nar.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {information theory; sequence logo; walker}
+ }
+
+ at ARTICLE{schoeniger1994,
+ AUTHOR = {Sch{\"o}niger, Michael and von Haeseler, Arndt},
+ YEAR = 1994,
+ TITLE = {A Stochastic Model for the Evolution of Autocorrelated {DNA} sequences},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 3,
+ PAGES = {240-247},
+ PDF = {schoeniger1994.mpe.pdf},
+ DOI = {10.1006/mpev.1994.1026},
+ PMID = {7529616},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{schoeniger1995,
+ AUTHOR = {Sch{\"o}niger, Michael and von Haeseler, Arndt},
+ YEAR = 1995,
+ TITLE = {Simulating efficiently the evolution of {DNA} sequences},
+ JOURNAL = {Comput. Appl. Biosci.},
+ VOLUME = 11,
+ PAGES = {111-115},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{schoeniger1995a,
+ AUTHOR = {Sch{\"o}niger, Michael and von Haeseler, Arndt},
+ YEAR = 1995,
+ TITLE = {Performance of the Maximum Likelihood, Neighbor Joining, and Maximum Parsimony Methods when Sequence Sites are not independent},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 44,
+ PAGES = {533-547},
+ PDF = {schoeniger1995a.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {maximum likelihood; neighbor joining; maximum parsimony; correlated sites; inconsistency; power of phylogenetic inferences; Felsenstein zone}
+ }
+
+ at ARTICLE{schoeniger1999,
+ AUTHOR = {Sch{\"o}niger, Michael and von Haeseler, Arndt},
+ YEAR = 1999,
+ TITLE = {Toward Assigning Helical Regions in Alignments of Ribosomal {RNA} and Testing the Appropriateness of Evolutionary Models},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 49,
+ PAGES = {691-698},
+ PDF = {schoeniger1999.jme.pdf},
+ DOI = {},
+ PMID = {10552050},
+ KEYWORDS = {Evolutionary models; Correlated sequence sites; Secondary structure; Alignment; Rate heterogeneity; Phylogenetic analysis; Maximum- likelihood inference; Monte Carlo simulation}
+ }
+
+ at ARTICLE{schuler1998,
+ AUTHOR = {Schuler, Gregory D.},
+ YEAR = 1998,
+ TITLE = {Sequence Mapping by Electronic {PCR}},
+ JOURNAL = {Genome Res.},
+ VOLUME = 7,
+ PAGES = {541-550},
+ PDF = {schuler1998.genome-res.pdf},
+ DOI = {},
+ PMID = {9149949},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{schulte1998,
+ AUTHOR = {Schulte II, James A. and Macey, J. Robert and Larson, Allan and Papenfuss, Theodore J.},
+ YEAR = 1998,
+ TITLE = {Molecular Tests of Phylogenetic Taxonomies: A General Procedure and Example Using Four Subfamilies of the Lizard Family Iguanidae},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 10,
+ PAGES = {367-376},
+ PDF = {schulte1998.mpe.pdf},
+ DOI = {10.1006/mpev.1998.0541},
+ PMID = {10051389},
+ KEYWORDS = {Reptilia; Squamata; Iguania; Iguanidae; Crotaphytinae; Iguaninae; Phrynosomatinae; Tropidurinae; Sator; mitochondrial DNA; phylogenetics; taxonomy; monophyly tests; metataxon}
+ }
+
+ at ARTICLE{scott2003,
+ AUTHOR = {Scott, Eugenie C. and Branch, Glenn},
+ YEAR = 2003,
+ TITLE = {Evolution: what's wrong with 'teaching the controversy'},
+ JOURNAL = {TREE},
+ VOLUME = 18,
+ PAGES = {499-502},
+ PDF = {scott2003.tree.pdf},
+ DOI = {10.1016/S0169-5347(03)00218-0},
+ PMID = {},
+ KEYWORDS = {Antievolutionism; teaching the controversy; Evolution}
+ }
+
+ at ARTICLE{searls2000,
+ AUTHOR = {Searls, David B.},
+ YEAR = 2000,
+ TITLE = {Bioinformatics Tools for Whole Genomes},
+ JOURNAL = {Annu. Rev. Genomics Hum. Genet.},
+ VOLUME = 1,
+ PAGES = {251-279},
+ PDF = {searls2000.annu-rev-genomics-hum-genet.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {genome analysis, algorithms, databases}
+ }
+
+ at ARTICLE{seberg2003,
+ AUTHOR = {Seberg, Ole and Humphries, Chris J. and Knapp, Sandy and Stevenson, Dennis Wm. and Petersen, Gitte and Scharff, Nikolaj and M{\o}ller Andersen, Nils},
+ YEAR = 2003,
+ TITLE = {Shortcuts in systematics? A commentary on {DNA}-based taxonomy},
+ JOURNAL = {TREE},
+ VOLUME = 18,
+ PAGES = {63-65},
+ PDF = {seberg2003.tree.pdf},
+ DOI = {10.1016/S0169-5347(02)00059-9},
+ PMID = {},
+ KEYWORDS = {systematics; DNA-based taxonomy}
+ }
+
+ at INPROCEEDINGS{segal2002,
+ AUTHOR = {Segal, Eran and Barash, Yoseph and Simon, Itamar and Friedman, Nir and Koller, Daphne},
+ YEAR = 2002,
+ TITLE = {From Promotor Sequence to Expression: A Probabilistic Framework},
+ BOOKTITLE = {Proceedings of RECOMB 2002},
+ MONTH = {},
+ ADDRESS = {},
+ PDF = {segal2002.RECOMB2002.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{segal2004,
+ AUTHOR = {Segal, Mark R. and Barbour, Jason D. and Grant, Robert M.},
+ YEAR = 2004,
+ TITLE = {Relating {HIV-1} Sequence Variation to Replication Capacity via Trees and Forests},
+ JOURNAL = {Stat. Appl. Genet. Mol. Biol.},
+ VOLUME = 3,
+ NUMBER = 1,
+ PAGES = {Article 2},
+ PDF = {segal2004.sagmb.pdf},
+ SOURCE = {http://www.bepress.com/sagmb/vol3/iss1/art2},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {HIV-1; Sequence Variation; Replication Capacity; Trees; Forests}
+ }
+
+ at ARTICLE{seligmann2003,
+ AUTHOR = {Seligmann, Herv\'{e}},
+ YEAR = 2003,
+ TITLE = {Cost-Minimization of Amino Acid Usage},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 56,
+ PAGES = {151-161},
+ PDF = {seligmann2003.jme.pdf},
+ DOI = {10.1007/s00239-002-2388-z},
+ PMID = {},
+ KEYWORDS = {Metabolic strategy; Sequence evolution; Codon bias; Developmental rate; Genome-size; Replacement rate; Endocellularity}
+ }
+
+ at ARTICLE{sellers1974,
+ AUTHOR = {Sellers, Peter H.},
+ YEAR = 1974,
+ TITLE = {On the Theory and Computation of Evolutionary Distances},
+ JOURNAL = {SIAM J. Appl. Math.},
+ VOLUME = 26,
+ PAGES = {787-793},
+ PDF = {sellers1974.siam-j-appl-math.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {evolutionary distances; alignment}
+ }
+
+ at ARTICLE{selosse2001,
+ AUTHOR = {Selosse, Marc-Andr\'{e} and Albert, B\'{e}atrice and Godelle, Bernard},
+ YEAR = 2001,
+ TITLE = {Organelle genome evolution (Response)},
+ JOURNAL = {TREE},
+ VOLUME = 16,
+ PAGES = {490},
+ PDF = {selosse2001.tree.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {genome size; asymmetical selection; mitochondria; organelle; Mytilus; gene transfer; mtDNA; endosymbiotic}
+ }
+
+ at ARTICLE{semerikov2003,
+ AUTHOR = {Semerikov, Vladimir L. and Zhang, Hengqing and Sun, Mei and Lascoux, Martin},
+ YEAR = 2003,
+ TITLE = {Conflicting phylogenies of \emph{Larix} ({Pinaceae}) based on cytoplasmic and nuclear {DNA}},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 27,
+ PAGES = {173-184},
+ PDF = {semerikov2003.mpe.pdf},
+ DOI = {10.1016/S1055-7903(02)00447-5},
+ PMID = {},
+ REMARK = {interessant, sollte man mal reinschaun},
+ KEYWORDS = {Larix; Chloroplast DNA; ITS; AFLP; Introgression; Incongruence}
+ }
+
+ at ARTICLE{semple2000,
+ AUTHOR = {Semple, Charles and Steel, Mike},
+ YEAR = 2000,
+ TITLE = {A supertree method for rooted trees},
+ JOURNAL = {Discr. Appl. Math.},
+ VOLUME = 105,
+ PAGES = {147-158},
+ PDF = {semple2000.discr-appl-math.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {supertrees;; Consensus; Rooted phylogenetic tree; Supertree}
+ }
+
+ at ARTICLE{semple2002,
+ AUTHOR = {Semple, Charles and Steel, Mike},
+ YEAR = 2002,
+ TITLE = {A characterization for a set of partial partitions to define an X-tree},
+ JOURNAL = {Discrete Math.},
+ VOLUME = 247,
+ PAGES = {169-186},
+ PDF = {semple2002.discrete-math.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {X-trees; Chordal graphs; Partition intersection graphs; Free X-trees}
+ }
+
+ at ARTICLE{semple2004,
+ AUTHOR = {Semple, Charles and Daniel, Philip and Hordijk, Wim and Page, Roderic D. M. and Steel, Mike},
+ YEAR = 2004,
+ TITLE = {Supertree Algorithms for Ancestral Divergence Dates and Nested Taxa},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 20,
+ PAGES = {in press},
+ PDF = {semple2004.bioinformatics-manuscript.pdf},
+ DOI = {10.1093/bioinformatics/btg},
+ PMID = {},
+ KEYWORDS = {supertrees;; }
+ }
+
+ at ARTICLE{seo2004,
+ AUTHOR = {Seo, Tae-Kun and Kishino, Hirohisa and Thorne, Jeffrey L.},
+ YEAR = 2004,
+ TITLE = {Estimating Absolute Rates of Synonymous and Nonsynonymous Nucleotide Substitution in Order to Characterize Natural Selection and Date Species Divergences},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 21,
+ PAGES = {1201-1213},
+ PDF = {seo2004.mbe.pdf},
+ DOI = {10.1093/molbev/msh088},
+ PMID = {15014159},
+ KEYWORDS = {Bayesian method; Markov chain Monte Carlo (MCMC); rate change model; lognormal; evolutionary rate; selection; synonymous rate; nonsynonymous rate}
+ }
+
+ at ARTICLE{shan2003,
+ AUTHOR = {Shan, Hongzhang and Singh, Jaswinder P. and Oliker, Leonid and Biswas, Rupak},
+ YEAR = 2003,
+ TITLE = {Message passing and shared address space parallelism on an SMP cluster},
+ JOURNAL = {Parallel Comput.},
+ VOLUME = 29,
+ PAGES = {167-186},
+ PDF = {shan2003.parallel-comput.pdf},
+ DOI = {10.1016/S0167-8191(02)00222-3},
+ PMID = {-},
+ KEYWORDS = {PC cluster; Message passing; Distributed shared memory; Benchmark applications; Parallel performance; parallel computing}
+ }
+
+ at ARTICLE{shankar1997,
+ AUTHOR = {Shankar, Ravi V. and Ranka, Sanjay},
+ YEAR = 1997,
+ TITLE = {Random Data Accesses on a Coarse-Grained Parallel Machine: I. One-to-One Mappings},
+ JOURNAL = {J. Parallel Distrib. Comput.},
+ VOLUME = 44,
+ PAGES = {14-23},
+ PDF = {shankar1997.jpdc.pdf},
+ DOI = {10.1006/jpdc.1997.1316},
+ PMID = {-},
+ KEYWORDS = {parallel computing}
+ }
+
+ at ARTICLE{shankar1997a,
+ AUTHOR = {Shankar, Ravi V. and Ranka, Sanjay},
+ YEAR = 1997,
+ TITLE = {Random Data Accesses on a Coarse-Grained Parallel Machine: {II.} One-to-Many and Many-to-One Mappings},
+ JOURNAL = {J. Parallel Distrib. Comput.},
+ VOLUME = 44,
+ PAGES = {24-34},
+ PDF = {shankar1997a.jpdc.pdf},
+ DOI = {10.1006/jpdc.1997.1315},
+ PMID = {-},
+ KEYWORDS = {parallel computing}
+ }
+
+ at ARTICLE{shao1986,
+ AUTHOR = {Shao, Jun},
+ YEAR = 1986,
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+ DOI = {},
+ PMID = {},
+ PAGES = {1322-1326}
+ }
+
+ at ARTICLE{shapiro2001,
+ AUTHOR = {Shapiro, Bruce A. and {Jin Chu Wu} and Bengali, David and Potts, Marc J.},
+ YEAR = 2001,
+ TITLE = {The massively parallel genetic algorithm for {RNA} folding: {MIMD} implementation and population variation},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 17,
+ PAGES = {137-148},
+ PDF = {shapiro2001.bioinformatics.pdf},
+ DOI = {},
+ PMID = {11238069},
+ KEYWORDS = {parallel bioinformatics; parallel computing; genetic algorithm; RNA folding}
+ }
+
+ at INPROCEEDINGS{shapiro2001a,
+ AUTHOR = {Shapiro, Bruce and Bengali, David and Kasprzak, Wojciech},
+ YEAR = 2001,
+ TITLE = {Determination of RNA folding pathway functional intermediates using a massively parallel genetic algorithm},
+ BOOKTITLE = {Proceedings of the 1st ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2001)},
+ PAGES = {1},
+ PUBLISHER = {ACM Press},
+ ADDRESS = {New York, NY, USA},
+ PDF = {shapiro2001a.BIOKDD2001.ps.gz},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel computing; parallel bioinformatics;; RNA folding; genetic algorithm}
+ }
+
+ at ARTICLE{sharman1999,
+ AUTHOR = {Sharman, Anna C.},
+ YEAR = 1999,
+ TITLE = {Some new terms for duplicated genes},
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+ DOI = {10.1006/scdb.1999.0338},
+ PMID = {},
+ KEYWORDS = {orthology; paralogy; pro-orthology; semi-orthology; trans-homology}
+ }
+
+ at ARTICLE{shaw1993,
+ AUTHOR = {Shaw, D. C. and Messer, M. and Scrivener, A. M. and Nicholas, K. R. and Griffiths, M.},
+ YEAR = 1993,
+ TITLE = {Isolation, partial characterisation, and amino acid sequence of alpha-lactalbumin from platypus ({Ornithorhynchus anatinus}) milk},
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+ YEAR = 2000,
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+ }
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+ at ARTICLE{simmons2001,
+ AUTHOR = {Simmons, Mark P. and Ochoterena, Helga and Carr, Timothy G.},
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+ }
+
+ at ARTICLE{simmons2001a,
+ AUTHOR = {Simmons, Nancy B.},
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+ }
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+ at ARTICLE{simmons2001b,
+ AUTHOR = {Simmons, Mark P. and Savolainen, Vincent and Clevinger, Curtis C. and Archer, Robert H. and Davis, Jerrold I.},
+ YEAR = 2001,
+ TITLE = {Phylogeny of the {Celastraceae} Inferred from {26S} Nuclear Ribosomal {DNA}, Phytochrome {B}, {rbcL}, {atpB}, and Morphology},
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+ PAGES = {353-366},
+ PDF = {simmons2001b.mpe.pdf},
+ DOI = {10.1006/mpev.2001.0937},
+ PMID = {},
+ KEYWORDS = {supertrees; multiple genes; phylogeny; Celastraceae}
+ }
+
+ at ARTICLE{simmons2002,
+ AUTHOR = {Simmons, Mark P. and Randle, Christopher P. and Freudenstein, John V. and Wenzel, John W.},
+ YEAR = 2002,
+ TITLE = {Limitations of Relative Apparent Synapomorphy Analysis ({RASA}) for Measuring Phylogenetic Signal},
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+ PDF = {simmons2002.mbe.pdf},
+ DOI = {},
+ PMID = {11752186},
+ KEYWORDS = {relative apparent synapomorphy analysis, RASA, phylogenetic signal, long-branch attraction, outgroup selection}
+ }
+
+ at ARTICLE{simmons2002a,
+ AUTHOR = {Simmons, Mark P. and Ochoterena, Helga and Freudenstein, John V.},
+ YEAR = 2002,
+ TITLE = {Amino acid vs. nucleotide characters: Challenging preconceived notions},
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+ PDF = {simmons2002a.mpe.pdf},
+ DOI = {10.1016/S1055-7903(02)00202-6},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{simmons2002b,
+ AUTHOR = {Simmons, Mark P. and Freudenstein, John V.},
+ YEAR = 2002,
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+ DOI = {10.1016/S1055-7903(02)00033-7},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{simmons2002c,
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+ JOURNAL = {Cladistics},
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+ DOI = {10.1006/clad.2002.0201},
+ PMID = {},
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+ }
+
+ at ARTICLE{simmons2002d,
+ AUTHOR = {Simmons, Mark P. and Ochoterena, Helga and Freudenstein, John V.},
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+ }
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+ }
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+ at ARTICLE{simmons2004a,
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+ DOI = {},
+ PMID = {10833190},
+ KEYWORDS = {phylogeny; maximum likelihood; maximum parsimony; site substitution models}
+ }
+
+ at ARTICLE{steel2000c,
+ AUTHOR = {Steel, Mike and Huson, Daniel and Lockhart, Peter J.},
+ YEAR = 2000,
+ TITLE = {Invariable Sites Models and Their Use in Phylogeny Reconstruction},
+ JOURNAL = {Syst. Biol.},
+ VOLUME = 49,
+ PAGES = {225-232},
+ PDF = {steel2000c.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Covariotide evolution; invariable sites; LogDet; sites free to vary}
+ }
+
+ at ARTICLE{steel2001,
+ AUTHOR = {Steel, M. and Hein, J.},
+ YEAR = 2001,
+ TITLE = {Applying the Thorne-Kishino-Felsenstein Model to Sequence Evolution on a Star-Shaped Tree},
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+ PAGES = {679-684},
+ PDF = {steel2001.appl-math-lett.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {DNA sequence evolution; Insertion-deletion model; Dynamic programming}
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+ at ARTICLE{stein2001,
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+ DOI = {10.1038/35080529},
+ PMID = {},
+ KEYWORDS = {}
+ }
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+ DOI = {},
+ PMID = {10093219},
+ KEYWORDS = {RNA editing; Pyrimidine exchange; Plant mitochondria; Bryophytes; Liverworts; Hornworts; Mosses; cox3; nad5}
+ }
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+ at ARTICLE{stellwag1999,
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+ PDF = {stellwag1999.scdb.pdf},
+ DOI = {10.1006/scdb.1999.0334},
+ PMID = {},
+ KEYWORDS = {gene duplication; Hox genes; evolution; teleosts; development}
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+ PDF = {stephens1985.mbe.pdf},
+ DOI = {},
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+
+ at INPROCEEDINGS{sterck2003,
+ AUTHOR = {De Sterck, H. and Markel, R. S. and Pohl, T. and R{\"u}de, U.},
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+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel computing; scientific computing;; Grid Computing; Tuple Spaces; Intertask Communication; Scalability; Java}
+ }
+
+ at ARTICLE{stern1999,
+ AUTHOR = {Stern, Michael D.},
+ TITLE = {Emergence of homeostasis and ``noise imprinting'' in an evolutionary model},
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+ KEYWORDS = {}
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+
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+ AUTHOR = {Stewart, Craig A. and Hart, David and Berry, Donald K. and Olsen, Gary J. and Wernert, Eric A. and Fischer, William},
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+ }
+
+ at ARTICLE{stibitz2000,
+ AUTHOR = {Stibitz, Thomas B. and Keeling, Patrick J. and Bhattacharya, Debashish},
+ YEAR = 2000,
+ TITLE = {Symbiotic Origin of a Novel Actin Gene in the Cryptophyte \textit{Pyrenomonas helgolandii}},
+ JOURNAL = {Mol. Biol. Evol.},
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+ PDF = {stibitz2000.mbe.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {actin evolution; cryptophytes; symbiosis; gene transfer; nucleomorph; phylogeny}
+ }
+
+ at ARTICLE{stiller2001,
+ AUTHOR = {Stiller, John W. and Riley, Jennifer and Hall, Benjamin D.},
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+ KEYWORDS = {Apocytochrome B; CTD; Cytochrome C oxidase; Elongation factor 2; Evolution; Green plants; Long-branch attraction; Mitochondria; Red algae; RPB1}
+ }
+
+ at ARTICLE{stiller1999,
+ AUTHOR = {Stiller, John W. and Hall, Benjamin D.},
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+ PDF = {stiller1999.mbe.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {amitochondriate amoebae; evolution; long-branch attraction; Mastigamoeba; phylogenetic; ssu rRNA}
+ }
+
+ at INPROCEEDINGS{stjohn2001,
+ AUTHOR = {St. John, Katherine and Warnow, Tandy and Moret, Bernard M. E. and Vawter, Lisa},
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+ PDF = {stjohn2001.SODA2001.pdf},
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+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{stoesser2002,
+ AUTHOR = {Stoesser, Guenter and Baker, Wendy and van den Broek, Alexandra and Camon, Evelyn and Garcia-Pastor, Maria and Kanz, Carola and Kulikova, Tamara and Leinonen, Rasko and Lin, Quan and Lombard, Vincent and Lopez, Rodrigo and Redaschi, Nicole and Stoehr, Peter and Tuli, Mary Ann and Tzouvara, Katerina and Vaughan, Robert},
+ YEAR = 2002,
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+ DOI = {},
+ PMID = {11752244},
+ KEYWORDS = {EMBL Nucleotide Sequence Database}
+ }
+
+ at ARTICLE{stoesser2003,
+ AUTHOR = {Stoesser, Guenter and Baker, Wendy and van den Broek, Alexandra and Garcia-Pastor, Maria and Kanz, Carola and Kulikova, Tamara and Leinonen, Rasko and Lin, Quan and Lombard, Vincent and Lopez, Rodrigo and Mancuso, Renato and Nardone, Francesco and Stoehr, Peter and Tuli, Mary Ann and Tzouvara, Katerina and Vaughan, Robert},
+ YEAR = 2003,
+ TITLE = {The {EMBL} Nucleotide Sequence Database: major new developments},
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+ DOI = {10.1093/nar/gkg021},
+ PMID = {12519939},
+ KEYWORDS = {EMBL Nucleotide Sequence Database}
+ }
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+ at ARTICLE{stoltzfus1999,
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+ PAGES = {169-181},
+ PDF = {stoltzfus1999.jme.pdf},
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+ PMID = {},
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+ }
+
+ at ARTICLE{storey2001,
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+ TITLE = {Future Trypanosomatid Phylogenies: Refined Homologies, Supertrees and Networks},
+ JOURNAL = {Mem. Inst. Oswaldo Cruz},
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+ VOLUME = 95,
+ PAGES = {523-526},
+ PDF = {stothard2000.mem-inst-oswaldo-cruz.pdf},
+ DOI = {},
+ PMID = {},
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+ PDF = {strimmer1996.mbe-bad.pdf},
+ DOI = {},
+ PMID = {},
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+ }
+
+ at ARTICLE{strimmer1996a,
+ AUTHOR = {Strimmer, Korbinian and von Haeseler, Arndt},
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+
+ at ARTICLE{strimmer1997,
+ AUTHOR = {Strimmer, Korbinian and Goldman, Nick and von Haeseler, Arndt},
+ YEAR = 1997,
+ TITLE = {Bayesian Probabilities and Quartet Puzzling},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 14,
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+ DOI = {},
+ PMID = {},
+ KEYWORDS = {accuracy; assigning penalties; Bayesian evaluation; posterior probabilities; quartet networks; quartet puzzling}
+ }
+
+ at ARTICLE{strimmer1997a,
+ AUTHOR = {Strimmer, Korbinian and von Haeseler, Arndt},
+ YEAR = 1997,
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+ DOI = {},
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+ KEYWORDS = {Likelihood-mapping; phylogenetic content visualization; phylogenetic cluster analysis}
+ }
+
+ at PHDTHESIS{strimmer1997b,
+ AUTHOR = {Strimmer, Korbinian S.},
+ YEAR = 1997,
+ TITLE = {Maximum Likelihood Methods in Molecular Phylogenetics},
+ SCHOOL = {Ludwig--Maximilians--Universit{\"a}t},
+ ADDRESS = {M{\"u}nchen, Germany},
+ PDF = {strimmer1997b.phdthesis.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{strimmer2000,
+ AUTHOR = {Strimmer, Korbinian and Moulton, Vincent},
+ YEAR = 2000,
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+ VOLUME = 17,
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+ PDF = {strimmer2000.mbe.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {phylogenetic networks;; maximum likelihood; phylogenetic network; graphical model; Bayesian network; evolutionary tree; Markov chain Monte Carlo sampling}
+ }
+
+ at ARTICLE{strimmer2001,
+ AUTHOR = {Strimmer, Korbinian and Wiuf, Carsten and Moulton, Vincent},
+ YEAR = 2001,
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+ DOI = {},
+ PMID = {11141198},
+ KEYWORDS = {ancestral recombination graph; likelihood-based sequence analysis; Bayesian network; phylogeny; split-graph}
+ }
+
+ at ARTICLE{strimmer2002,
+ AUTHOR = {Strimmer, Korbinian and Rambaut, Andrew},
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+ DOI = {10.1098/rspb.2001.1862},
+ PMID = {11798428},
+ KEYWORDS = {model selection; model misspecification; confidence set; expected likelihood weight; ELW; bootstrap; variance reduction}
+ }
+
+ at ARTICLE{strimmer2003,
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+ PDF = {struck2003.mpe.pdf},
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+ PMID = {},
+ REMARK = {interessant, sollte man mal reinschaun},
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+ }
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+ at ARTICLE{suchard2001,
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+ at ARTICLE{suchard2002,
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+ at ARTICLE{suchard2003,
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+ PAGES = {723-729},
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+ DOI = {},
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+ at ARTICLE{sunnucks2000,
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+ PMID = {},
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+ at ARTICLE{susko2002,
+ AUTHOR = {Susko, Edward and Inagaki, Yuji and Field, Chris and Holder, Michael E. and Roger, Andrew J.},
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+ PDF = {susko2002.mbe.pdf},
+ DOI = {},
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+
+ at ARTICLE{susko2003,
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+ PAGES = {862-868},
+ PDF = {susko2003.mbe.pdf},
+ DOI = {10.1093/molbev/msg093},
+ PMID = {12716999},
+ KEYWORDS = {generalized least squares; phylogeny; statistical tests}
+ }
+
+ at ARTICLE{suzuki2002,
+ AUTHOR = {Suzuki, Yoshiyuki and Nei, Masatoshi},
+ YEAR = 2002,
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+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 19,
+ PAGES = {1865-1869},
+ PDF = {suzuki2002.mbe.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {positive selection; parsimony; binomial probability; likelihood; posterior probability}
+ }
+
+ at ARTICLE{suzuki2004,
+ AUTHOR = {Suzuki, Yoshiyuki and Nei, Masatoshi},
+ YEAR = 2004,
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+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 21,
+ PAGES = {914-921},
+ PDF = {suzuki2004.mbe.pdf},
+ DOI = {10.1093/molbev/msh098},
+ PMID = {15014169},
+ KEYWORDS = {Positive selection; parsimony; likelihood; Thalassiosira weissflogii; sexually induced gene 1; human T-cell lymphotropic virus type I; tax}
+ }
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+ at ARTICLE{swiderski1998,
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+ at INCOLLECTION{swofford1990,
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+ TITLE = {{PAUP}: Phylogenetic analysis using parsimony, {V}3.1.1.},
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+ ADDRESS = {Washington, D.C.}
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+ at INCOLLECTION{swofford1996,
+ AUTHOR = {Swofford, David L. and Olsen, Gary J. and Waddell, Peter J. and Hillis, David M.},
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+ ADDRESS = {Sunderland, Massachusetts}
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+ DOI = {},
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+ }
+
+ at ARTICLE{swofford2001,
+ AUTHOR = {Swofford, David L. and Waddell, Peter J. and Huelsenbeck, John P. and Foster, Peter G. and Lewis, Paul O. and Rogers, James S.},
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+ at ARTICLE{symonds2002,
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+ YEAR = 2002,
+ TITLE = {The Effects of Topological Inaccuracy in Evolutionary Trees on the Phylogenetic Comparative Method of Independent Contrasts},
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+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {10.1080/10635150290069977},
+ PMID = {},
+ KEYWORDS = {Comparative method; computer simulation; independent contrasts; phylogenetic error; random phylogenies; topological inaccuracy}
+ }
+
+ at ARTICLE{sytsma2001,
+ AUTHOR = {Sytsma, K. J. and Pires, J. C.},
+ YEAR = 2001,
+ TITLE = {Plant systematics in the next 50 years -- re-mapping the new frontier},
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+ DOI = {},
+ PMID = {},
+ KEYWORDS = {phylogenetics, pluralism, systematics, taxonomy}
+ }
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+ YEAR = 2002,
+ TITLE = {Rates of Ribosomal {RNA} Evolution Are Uniquely Accelerated in Eukaryotes},
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+ PDF = {syvanen2002.jme.pdf},
+ DOI = {10.1007/s00239-001-2306-9},
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+ KEYWORDS = {Ribosomal ssu rRNA, rps11, rp114, Distance-matrix, Stochastic clock, Longevity sensor}
+ }
+
+ at ARTICLE{szczepanik2001,
+ AUTHOR = {Szczepanik, Dorota and Mackiewicz, Pawe{\l} and Kowalczuk, Maria and Gierlik, Agnieszka and Nowicka, Aleksandra and Dudek, Miros{\l}aw R. and Cebrat, Stanis{\l}aw},
+ YEAR = 2001,
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+ DOI = {10.1007/s002390010172},
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+ KEYWORDS = {Orthologs; DNA asymmetry; Mutation pressure; Evolution rate}
+ }
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+ PMID = {},
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+ AUTHOR = {Takahashi, Kei and Nei, Masatoshi},
+ YEAR = 2000,
+ TITLE = {Efficiencies of Fast Algorithms of Phylogenetic Inference Under the Criteria of Maximum Parsimony, Minimum Evolution, and Maximum Likelihood When a Large Number of Sequences Are Used},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 17,
+ PAGES = {1251-1258},
+ PDF = {takahashi2000.mbe.pdf},
+ DOI = {},
+ PMID = {10908645},
+ KEYWORDS = {phylogenetic inference, maximum parsimony, minimum evolution, maximum likelihood, topological distance, tree-building algorithms}
+ }
+
+ at ARTICLE{tajima1994,
+ AUTHOR = {Tajima, Fumio and Takezaki, Naoko},
+ YEAR = 1994,
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+ PDF = {tajima1994.mbe.pdf},
+ DOI = {},
+ PMID = {8170368},
+ KEYWORDS = {DNA sequences; evolutionary distance; molecular phylogenetic tree; Jukes and Cantor's method; Kimura's method; transition/transversion bias}
+ }
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+ at ARTICLE{takemura2001,
+ AUTHOR = {Takemura, Masaharu},
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+ TITLE = {Poxviruses and the Origin of the Eukaryotic Nucleus},
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+ DOI = {10.1007/s002390010171},
+ PMID = {11443345},
+ KEYWORDS = {DNA polymerase alpha; DNA polymerase delta; DNA replication; Molecular evolution; Phylogenetic tree; Poxvirus; Eukaryotic nucleus}
+ }
+
+ at ARTICLE{takezaki1994,
+ AUTHOR = {Takezaki, Naoko and Nei, Masatoshi},
+ YEAR = 1994,
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+ YEAR = 1995,
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+ DOI = {},
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+ KEYWORDS = {molecular clock; linearized tree; estimation of divergence time; phylogetic trees; hominoid evolution; Drosophilids}
+ }
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+ at ARTICLE{takezaki1998,
+ AUTHOR = {Takezaki, Naoko},
+ YEAR = 1998,
+ TITLE = {Tie Trees Generated by Distance Methods of Phylogenetic Reconstruction},
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+ DOI = {},
+ PMID = {9615454},
+ KEYWORDS = {tie trees; phylogenetic analysis; distance methods; neighbor-joining method; UPGMA}
+ }
+
+ at ARTICLE{takezaki1999,
+ AUTHOR = {Takezaki, Naoko and Gojobori, Takashi},
+ YEAR = 1999,
+ TITLE = {Correct and Incorrect Vertebrate Phylogeneties Obtained by the Entire Mitochondrial {DNA} Sequences},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 16,
+ PAGES = {590-601},
+ PDF = {takezaki1999.mbe.pdf},
+ DOI = {},
+ PMID = {10335652},
+ KEYWORDS = {mitochondrial phylogeny; tree-making methods; rate variation across sites; amino acid composition; hydrophobic amino acid}
+ }
+
+ at ARTICLE{takezaki2003,
+ AUTHOR = {Takezaki, Naoko and Figueroa, Felipe and Zaleska-Rutczynska, Zofia and Klein, Jan},
+ YEAR = 2003,
+ TITLE = {Molecular Phylogeny of Early Vertebrates: Monophyly of the Agnathans as Revealed by Sequences of 35 Genes },
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 20,
+ PAGES = {287-292},
+ PDF = {takezaki2003.mbe.pdf},
+ SUPPL = {takezaki2003.3066_align_s.txt, takezaki2003.addon2.pdf, takezaki2003.3066_align_t.txt, takezaki2003.addon3.pdf, takezaki2003.addon1.pdf},
+ DOI = {10.1093/molbev/msg040},
+ PMID = {12598696},
+ KEYWORDS = {molecular phylogeny; lamprey; hagfish; cartilaginous fish; bony fish}
+ }
+
+ at ARTICLE{tamura1993,
+ AUTHOR = {Tamura, Koichiro and Nei, Masatoshi},
+ YEAR = 1993,
+ TITLE = {Estimation of the Number of Nucleotide Substitutions in the Control Region of Mitochondrial {DNA} in Humans and Chimpanzees},
+ JOURNAL = {Mol. Biol. Evol.},
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+ PAGES = {512-526},
+ PDF = {tamura1993.mbe.pdf},
+ DOI = {},
+ PMID = {8336541},
+ KEYWORDS = {mtDNA control region; nucleotide substitutions; transition/transversion bias; human evolution; chimpanzees}
+ }
+
+ at ARTICLE{tamura1996,
+ AUTHOR = {Tamura, Koichiro},
+ YEAR = 1996,
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+ DOI = {},
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+ }
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+ at ARTICLE{tamura2002,
+ AUTHOR = {Tamura, Koichiro and Kumar, Sudhir},
+ YEAR = 2002,
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+ DOI = {10.1093/bioinformatics/btg1042},
+ PMID = {},
+ KEYWORDS = {accurate phylogenetic reconstruction; gene-order data}
+ }
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+ at ARTICLE{tateno1994,
+ AUTHOR = {Tateno, Yoshio and Takezaki, Naoko and Nei, Masatoshi},
+ YEAR = 1994,
+ TITLE = {Relative Efficiencies of the Maximum--Likelihood, Neighbor--Joining, and Maximum--Parsimony Methods When Substitution Rate Varies with Site},
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+ PDF = {tateno1994.mbe.pdf},
+ DOI = {},
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+ AUTHOR = {Tavar{\'e}, Simon},
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+ TITLE = {Single Eubacterial Origin of Eukaryotic Sulfide:Quinone Oxidoreductase, a Mitochondrial Enzyme Conserved from the Early Evolution of Eukaryotes During Anoxic and Sulfidic Times},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 20,
+ PAGES = {1564-1574},
+ PDF = {theissen2003.mbe.pdf},
+ DOI = {10.1093/molbev/msg174},
+ PMID = {12832624},
+ KEYWORDS = {sulfide-quinone reductase; endosymbiosis; hydrogenosomes; electron transport chain; anaerobiosis}
+ }
+
+ at ARTICLE{theys2001,
+ AUTHOR = {Theys, Mitchell D. and Ali, Shoukat and Siegel, Howard Jay and Chandy, Mani and Hwang, Kai and Kennedy, Ken and Sha, Lui and Shin, Kang G. and Snir, Marc and Snyder, Larry and Sterling, Thomas},
+ YEAR = 2001,
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+ }
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+ PDF = {thomas2004.mpe.pdf},
+ DOI = {10.1016/S1055-7903(03)00222-7},
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+ KEYWORDS = {parsimony, Bayesian, minimum evolution, quartet puzzling}
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+ MONTH = {July},
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+ DOI = {},
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+ AUTHOR = {Thorley, Joseph L.},
+ YEAR = 2000,
+ TITLE = {Cladistic Information, Leaf Stability And Supertree Construction},
+ SCHOOL = {Department of Biological Sciences, Faculty of Science, University of Bristol},
+ ADDRESS = {UK},
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+ at ARTICLE{thorne1992,
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+
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+ AUTHOR = {Thorne, Jeffrey L. and Kishino, Hirohisa},
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+ }
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+ at ARTICLE{thorne1992b,
+ AUTHOR = {Thorne, Jeffrey L. and Kishino, Hirohisa and Felsenstein, Joseph},
+ YEAR = 1992,
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+ }
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+ at ARTICLE{thorne1998,
+ AUTHOR = {Thorne, Jeffrey L. and Kishino, Hirohisa and Painter, Ian S.},
+ YEAR = 1998,
+ TITLE = {Estimating the Rate of Evolution of the Rate of Molecular Evolution},
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+ at ARTICLE{thorne2002,
+ AUTHOR = {Thorne, Jeffrey L. and Kishino, Hirohisa},
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+ at ARTICLE{whelan2001a,
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+ at ARTICLE{wilkinson1996,
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+ at INPROCEEDINGS{williams2003a,
+ AUTHOR = {Williams, Tiffani L. and Moret, Bernard M. E.},
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+
+ at TECHREPORT{williams2004,
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+ INSTITUTION = {University New Mexico},
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+ TYPE = {UNM Computer Science Tech-Reports},
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+ DOI = {10.1016/S1055-7903(02)00326-3},
+ PMID = {},
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+ at ARTICLE{xia2003,
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+ AUTHOR = {Yang, Ziheng},
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+ at ARTICLE{yang1994c,
+ AUTHOR = {Yang, Ziheng and Kumar, Sudhir},
+ YEAR = 1994,
+ TITLE = {Approximate Methods for Estimating the Pattern of Nucleotide Substitution and the Variation of Substitution Rates Among Sites},
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+
+ at ARTICLE{yang1996,
+ AUTHOR = {Yang, Ziheng},
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+
+ at ARTICLE{yang1996a,
+ AUTHOR = {Yang, Ziheng},
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+ at ARTICLE{yang1996b,
+ AUTHOR = {Yang, Ziheng and Kumar, Sudhir},
+ YEAR = 1996,
+ TITLE = {Approximate Methods for Estimating the Pattern of Nucleotide Substitution and the Variation of Substitution Rates Among Sites},
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+ }
+
+ at ARTICLE{yang1997,
+ AUTHOR = {Yang, Hong and Golenberg, Edward M. and Shoshani, Jeheskel},
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+ at ARTICLE{yang1997a,
+ AUTHOR = {Yang, Ziheng and Rannala, Bruce},
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+ TITLE = {Likelihood Ratio Tests for Detecting Positive Selection and Application to Primate Lysozyme Evolution},
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+
+ at ARTICLE{yang1997c,
+ AUTHOR = {Yang, Ziheng},
+ YEAR = 1997,
+ TITLE = {{PAML}: A program package for phylogenetic analysis by maximum likelihood},
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+ at ARTICLE{yang1998,
+ AUTHOR = {Yang, Ziheng},
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+ TITLE = {Likelihood Ratio Tests for Detecting Positive Selection and Application to Primate Lysozyme Evolution},
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+ PDF = {yang1998.mbe.pdf},
+ DOI = {},
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+ KEYWORDS = {positive selection; episodic evolution; neutral theory; lysozyme; primates; maximum likelihood; likelihood ratio test; synonymous rates; nonsynonymous rates}
+ }
+
+ at ARTICLE{yang1998a,
+ AUTHOR = {Ziheng Yang and Rasmus Nielsen},
+ YEAR = 1998,
+ TITLE = {Synonymous and Nonsynonymous Rate Variation in Nuclear Genes of Mammals},
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+ DOI = {},
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+ KEYWORDS = {synonymous rates; nonsynonymous rates; mammalian genes; likelihood; codon substitution; transition/transversion rate bias; neutral theory}
+ }
+
+ at ARTICLE{yang1998b,
+ AUTHOR = {Ziheng Yang and Rasmus Nielsen and Hasegawa, Masami},
+ YEAR = 1998,
+ TITLE = {Models of Amino Acid Substitution and Application to Mitochondrial Protein Evolution},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 15,
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+ PDF = {yang1998b.mbe.pdf},
+ DOI = {},
+ PMID = {9866196},
+ KEYWORDS = {amino acid substitution; mammals; maximum likelihood; mitochondrial DNA; protein evolution}
+ }
+
+ at ARTICLE{yang1998c,
+ AUTHOR = {Yang, Ziheng},
+ YEAR = 19988,
+ TITLE = {On the Best Evolutionary Rate for Phylogenetic Analysis},
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+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Branch lengths; homoplasy; likelihood; par simony; phylogeny; optimum evolutionary rate; saturation; simulation}
+ }
+
+ at ARTICLE{yang1999,
+ AUTHOR = {Yang, Ziheng and Yoder, Anne D.},
+ YEAR = 1999,
+ TITLE = {Estimation of the Transition/Transversion Rate Bias and Species Sampling},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 48,
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+ DOI = {},
+ PMID = {10093216},
+ KEYWORDS = {Transition/transversion rate ratio; Maximum likelihood; Species sampling; Saturation; Lemurs; Primates}
+ }
+
+ at ARTICLE{yang2000,
+ AUTHOR = {Yang, Ziheng},
+ YEAR = 2000,
+ TITLE = {Maximum Likelihood Estimation on Large Phylogenies and Analysis of Adaptive Evolution in Human Influenza Virus {A}},
+ JOURNAL = {J. Mol. Evol.},
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+ PAGES = {423-432},
+ PDF = {yang2000.jme.pdf},
+ DOI = {10.1007/s002390010105},
+ PMID = {11080365},
+ KEYWORDS = {Large phylogenies; Maximum likelihood; Molecular adaptation; Nonsynonymous substitution; Phylogenetics; Positive selection; Synonymous substitution}
+ }
+
+ at ARTICLE{yang2000a,
+ AUTHOR = {Yang, Ziheng and Bielawski, Joseph P.},
+ YEAR = 2000,
+ TITLE = {Statistical methods for detecting molecular adaptation},
+ JOURNAL = {TREE},
+ VOLUME = 15,
+ PAGES = {496-503},
+ PDF = {yang2000a.tree.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{yang2000b,
+ AUTHOR = {Yang, Ziheng and R. Nielsen and N. Goldman and A.-M. K. Pedersen},
+ YEAR = 2000,
+ TITLE = {Codon-substitution models for heterogeneous selection pressure at amino acid sites},
+ JOURNAL = {Genetics},
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+ PAGES = {431-449},
+ PDF = {},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
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+
+ at ARTICLE{yang2002,
+ AUTHOR = {Yang, Ziheng and Swanson, Willie J.},
+ YEAR = 2002,
+ TITLE = {Codon-Substitution Models to Detect Adaptive Evolution that Account for Heterogeneous Selective Pressures Among Site Classes},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 19,
+ PAGES = {49-57},
+ PDF = {yang2002.mbe.pdf},
+ DOI = {},
+ PMID = {11752189},
+ KEYWORDS = {synonymous rate; nonsynonymous rate; positive selection; partitioned data; lysin; MHC; maximum likelihood; Bayes}
+ }
+
+ at ARTICLE{yang2002a,
+ AUTHOR = {Yang, Ziheng and Nielsen, Rasmus},
+ YEAR = 2002,
+ TITLE = {Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 19,
+ PAGES = {908-917},
+ PDF = {yang2002a.mbe.pdf},
+ DOI = {},
+ PMID = {12032247},
+ KEYWORDS = {gene duplication; maximum likelihood; molecular adaptation; nonsynonymous substitution; positive selection; synonymous substitution}
+ }
+
+ at ARTICLE{yang2002b,
+ AUTHOR = {Yang, Yee Hwa and Speed, Terry},
+ YEAR = 2002,
+ TITLE = {Design Issues for {cDNA} Microarray Experiments},
+ JOURNAL = {Nat. Rev. Genet.},
+ VOLUME = 3,
+ PAGES = {579-588},
+ PDF = {yang2002b.nat-rev-genet.pdf},
+ DOI = {10.1038/nrg863},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{yang2002c,
+ AUTHOR = {Yang, Yau-Wen and Chen, Ying and Li, Wen-Hsiung},
+ YEAR = 2002,
+ TITLE = {The Influence of Adjacent Nucleotides on the Pattern of Nucleotide Substitution in Mitochondrial Introns of Angiosperms},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 55,
+ PAGES = {111-115},
+ PDF = {yang2002c.jme.pdf},
+ DOI = {10.1007/s00239-001-2310-0},
+ PMID = {},
+ KEYWORDS = {Nucleotide substitution pattern, Mitochondrial DNA, Chloroplast DNA, Sequence context effect}
+ }
+
+ at ARTICLE{yang2002d,
+ AUTHOR = {Yang, Ziheng},
+ YEAR = 2002,
+ TITLE = {Inference of selection from multiple species alignments},
+ JOURNAL = {Curr. Opin. Genet. Dev.},
+ VOLUME = 12,
+ PAGES = {688-694},
+ PDF = {yang2002d.curr-opin-genet-dev.pdf},
+ DOI = {10.1016/S0959-437X(02)00348-9},
+ PMID = {},
+ KEYWORDS = {adaptive evolution; positive selection; protein evolution; codon substitution models; maximum likelihood; ancestral reconstruction; synonymous substitution; nonsynonymous substitution}
+ }
+
+ at INPROCEEDINGS{yang2003,
+ AUTHOR = {Yang, Laurence Tianruo and Brent, Richard P.},
+ YEAR = 2003,
+ TITLE = {Parallel {MCGLS} and {ICGLS} Methods for Least Squares Problems on Distributed Memory Architectures},
+ BOOKTITLE = {Proceedings of the International Symposium Parallel and Distributed Processing and Applications (ISPA 2003)},
+ PAGES = {197-208},
+ SERIES = {Lecture Notes in Computer Science},
+ VOLUME = 2745,
+ MONTH = {July},
+ PUBLISHER = {Springer},
+ ADDRESS = {Heidelberg},
+ PDF = {yang2003.lncs.pdf},
+ DOI = {},
+ PMID = {-},
+ KEYWORDS = {parallel computing;; least square methods}
+ }
+
+ at ARTICLE{yap1998,
+ AUTHOR = {Yap, T. and Frieder, O. and Martino, R.},
+ YEAR = 1998,
+ TITLE = {Parallel computation in biological sequence analysis},
+ JOURNAL = {IEEE Trans. Parallel Distrib. Syst.},
+ VOLUME = 9,
+ PAGES = {283-293},
+ PDF = {yap1998.tpds.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {parallel bioinformatics; parallel computing}
+ }
+
+ at ARTICLE{yashina2001,
+ AUTHOR = {Yashina, Lyudmila and Mishin, Vasiliy and Zdanovskaya, Nina and Schmaljohn, Connie and Ivanov, Leonid},
+ YEAR = 2001,
+ TITLE = {A Newly Discovered Variant of a {Hantavirus} in {Apodemus peninsulae}, Far Eastern {Russia}},
+ JOURNAL = {Emerg. Infect. Dis.},
+ VOLUME = 7,
+ PAGES = {912-913},
+ PDF = {yashina2001.emerg-infect-dis.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Hantavirus; Apodemus peninsulae; Far Eastern Russia}
+ }
+
+ at ARTICLE{ye2003,
+ AUTHOR = {Ye, Yuzhen and Jaroszewski, Lukasz and Li, Weizhong and Godzik, Adam},
+ YEAR = 2003,
+ TITLE = {A segment alignment approach to protein comparison},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 19,
+ PAGES = {742-749},
+ PDF = {ye2003.bioinformatics.pdf},
+ DOI = {10.1093/bioinformatics/btg073},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{yoccoz2001,
+ AUTHOR = {Yoccoz, Nigel G. and Nichols, James D. and Boulinier, Thierry},
+ YEAR = 2001,
+ TITLE = {Monitoring of biological diversity in space and time},
+ JOURNAL = {TREE},
+ VOLUME = 16,
+ PAGES = {446-453},
+ PDF = {yoccoz2001.tree.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {adaptive management; detection error; probability sampling; weak inference; strong inference; biological diversity}
+ }
+
+ at ARTICLE{yoder2000,
+ AUTHOR = {Yoder, Anne D. and Yang, Ziheng},
+ YEAR = 2000,
+ TITLE = {Estimation of Primate Speciation Dates Using Local Molecular Clocks},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 17,
+ PAGES = {1081-1090},
+ PDF = {yoder2000.mbe.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {local molecular clock; maximum likelihood; mitochondrial; DNA; molecular clock; primates; mammals; speciation dates}
+ }
+
+ at INPROCEEDINGS{yoshikawa1999,
+ AUTHOR = {Yoshikawa, Takanobu and Tabe, Tomohiro and Kishinami, Risa and Matsuda, Hideo and Hashimoto, Akihiro},
+ YEAR = 1999,
+ TITLE = {On the Implementation of a Phylogenetic Tree Database},
+ BOOKTITLE = {Proceedings of the IEEE Pacific Rim Conference on Communications, Computers, and Signal Processing},
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+ MONTH = {August},
+ PDF = {NICHT VORHANDEN, TODO},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Phylogenetic Tree; Database}
+ }
+
+ at ARTICLE{yu2002,
+ AUTHOR = {Yu, Yi-Kuo and Bundschuh, Ralf and Hwa, Terence},
+ YEAR = 2002,
+ TITLE = {Hybrid alignment: High-performance with universal statistics},
+ JOURNAL = {Bioinformatics},
+ VOLUME = 18,
+ PAGES = {864-872},
+ PDF = {yu2002.bioinformatics.pdf},
+ DOI = {},
+ PMID = {12075022},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{yue1998,
+ AUTHOR = {Yue, Kelvin K. and Lilja, David J.},
+ YEAR = 1998,
+ TITLE = {Comparing Processor Allocation Strategies in Multiprogrammed Shared-Memory Multiprocessors},
+ JOURNAL = {J. Parallel Distrib. Comput.},
+ VOLUME = 49,
+ PAGES = {245-258},
+ PDF = {yue1998.jpdc.pdf},
+ DOI = {10.1006/jpdc.1998.1443},
+ PMID = {-},
+ KEYWORDS = {parallel computing; scheduling; processor allocation}
+ }
+
+ at ARTICLE{yule1924,
+ AUTHOR = {Yule, G. Udny},
+ YEAR = 1924,
+ TITLE = {A Mathematical Theory of Evolution, Based on the Conclusions of {Dr. J. C. Willis, F.R.S.}},
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+ PDF = {yule1924.phil-trans-rsoc-b.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Theory of Evolution; Birth-Process}
+ }
+
+
+ at ARTICLE{zachariasen1999,
+ AUTHOR = {Zachariasen, M. and Winter, P.},
+ YEAR = 1999,
+ TITLE = {Concatenation-Based Greedy Heuristics for the Euclidean Steiner Tree Problem},
+ JOURNAL = {Algorithmica},
+ VOLUME = 25,
+ PAGES = {418-437},
+ PDF = {zachariasen1999.algorithmica.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{zaki1997,
+ AUTHOR = {Zaki, Mohammed Javeed and Li, Wei and Parthasarathy, Srinivasan},
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+ PDF = {zaki1997.jpdc.pdf},
+ DOI = {10.1006/jpdc.1997.1339},
+ PMID = {-},
+ KEYWORDS = {parallel computing; dynamic load balancing; network of workstations}
+ }
+
+ at ARTICLE{zamocky2000,
+ AUTHOR = {Z\'{a}mock\'{y}, Marcel and Janei\u{c}ek, \u{S}tefan and Koller, Franz},
+ YEAR = 2000,
+ TITLE = {Common phylogeny of catalase-peroxidases and ascorbate peroxidases},
+ JOURNAL = {Gene},
+ VOLUME = 256,
+ PAGES = {169-182},
+ PDF = {zamocky2000.gene.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Catalase; Cytochrome c peroxidase; Gene duplication; Hydrophobic cluster analysis; Unrooted phylogenetic tree}
+ }
+
+ at ARTICLE{zander1998,
+ AUTHOR = {Zander, Richard H.},
+ YEAR = 1998,
+ TITLE = {Phylogenetic reconstruction, a critique},
+ JOURNAL = {Taxon},
+ VOLUME = 47,
+ PAGES = {681-693},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{zander2001,
+ AUTHOR = {Zander, Richard H.},
+ YEAR = 2001,
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+ JOURNAL = {Syst. Biol.},
+ VOLUME = 50,
+ PAGES = {425-437},
+ PDF = {zander2001.syst-biol.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Branch length; chi-squared; Didymodon; multiple gene trees; primates; probabilistic reconstruction; support}
+ }
+
+ at ARTICLE{zeeberg2002,
+ AUTHOR = {Zeeberg, Barry},
+ YEAR = 2002,
+ TITLE = {Shannon Information Theoretic Computation of Synonymous Codon Usage Biases in Coding Regions of Human and Mouse Genomes},
+ JOURNAL = {Genome Res.},
+ VOLUME = 12,
+ PAGES = {944-955},
+ PDF = {zeeberg2002.genome-res.pdf},
+ DOI = {10.1101/gr.213402},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{zerges2000,
+ AUTHOR = {Zerges, William},
+ YEAR = 2000,
+ TITLE = {Translation in chloroplasts},
+ JOURNAL = {Biochimie},
+ VOLUME = 82,
+ PAGES = {683-601},
+ PDF = {zerges2000.biochimie.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {translation; chloroplasts; mRNA; ribosome; organelle}
+ }
+
+ at INPROCEEDINGS{zhang1989,
+ AUTHOR = {Zhang, Xiru and Waltz, David and Mesirov, Jill P.},
+ YEAR = 1989,
+ TITLE = {Protein structure prediction by a data-level parallel algorithm},
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+ ADDRESS = {New York, USA},
+ PDF = {zhang1989.SC.pdf},
+ DOI = {10.1145/76263.76286},
+ PMID = {},
+ KEYWORDS = {parallel computing; parallel bioinformatics;; protein structure prediction; computational biology; memory-based reasoning; data-level parallelism}
+ }
+
+ at ARTICLE{zhang1996,
+ AUTHOR = {Zhang, Z. and He, B. and Miller, W.},
+ YEAR = 1996,
+ TITLE = {Local multiple alignment via subgraph enumeration},
+ JOURNAL = {Discr. Appl. Math.},
+ VOLUME = 71,
+ PAGES = {337-365},
+ PDF = {zhang1996.discr-appl-math.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {Sequence comparison; Multiple alignment; Subgraph enumeration; Maximal clique}
+ }
+
+ at ARTICLE{zhang1998,
+ AUTHOR = {Zhang, Jianzhi and Gu, Xun},
+ YEAR = 1998,
+ TITLE = {Correlation Between the Substitution Rate and Rate Variation Among Sites in Protein Evolution},
+ JOURNAL = {Genetics},
+ VOLUME = 149,
+ PAGES = {1615-1625},
+ PDF = {zhang1998.genetics.pdf},
+ DOI = {},
+ PMID = {9649548},
+ KEYWORDS = {Substitution Rate; Rate Variation; Protein Evolution}
+ }
+
+ at ARTICLE{zhang1999,
+ AUTHOR = {Zhang, Jianzhi},
+ TITLE = {Performance of Likelihood Ratio Tests of Evolutionary Hypotheses Under Inadequate Substitution Models},
+ JOURNAL = {Mol. Biol. Evol.},
+ YEAR = 1999,
+ VOLUME = 16,
+ PAGES = {868-875},
+ PDF = {zhang1999.mbe.pdf},
+ DOI = {},
+ PMID = {10368963},
+ KEYWORDS = {likelihood ratio test; substitution models; molecular clock; transition/transversion bias; rate variation among sites; molecular evolution}
+ }
+
+ at ARTICLE{zhang2000,
+ AUTHOR = {Zhang, Weiping},
+ YEAR = 2000,
+ TITLE = {Phylogeny of the Grass Family (Poaceae) from rpl16 Intron Sequence Data},
+ JOURNAL = {Mol. Phylogenet. Evol.},
+ VOLUME = 15,
+ PAGES = {135-146},
+ PDF = {zhang2000.mpe.pdf},
+ DOI = {10.1006/mpev.1999.0729},
+ PMID = {10764541},
+ KEYWORDS = {rpl16 intron sequences; grass; phylogeny }
+ }
+
+ at MASTERSTHESIS{zhang2000a,
+ AUTHOR = {Zhang, Haoyong},
+ YEAR = 2000,
+ TITLE = {Design, implementation, and analysis of a novel quartet-based phylogenetic reconstruction method},
+ SCHOOL = {Department of Computer Science, University of Waterloo},
+ ADRESS = {Ontario, Canada},
+ PDF = {zhang2000a.mastersthesis.ps},
+ DOI = {-},
+ PMID = {-},
+ KEYWORDS = {quartets; phylogenetic reconstruction method}
+ }
+
+ at ARTICLE{zhang2002,
+ AUTHOR = {Zhang, Jian},
+ YEAR = 2002,
+ TITLE = {Analysis of Information Content for Biological Sequences},
+ JOURNAL = {J. Comput. Biol.},
+ VOLUME = 9,
+ PAGES = {487-503},
+ PDF = {zhang2002.jcb.pdf},
+ DOI = {},
+ PMID = {},
+ KEYWORDS = {information content; multiple alignment; analysis-of-variance ; RNA-binding motifs}
+ }
+
+ at ARTICLE{zhang2002a,
+ AUTHOR = {Zhang, Michael Q.},
+ YEAR = 2002,
+ TITLE = {Computational Prediction of Eukaryotic Protein-Coding Genes},
+ JOURNAL = {Nat. Rev. Genet.},
+ VOLUME = 3,
+ PAGES = {698-710},
+ PDF = {zhang2002.nat-rev-genet.pdf},
+ DOI = {10.1038/nrg890},
+ PMID = {},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{zhang2003,
+ AUTHOR = {Zhang, Jianzhi},
+ YEAR = 2003,
+ TITLE = {Evolution by gene duplication: an update},
+ JOURNAL = {TREE},
+ VOLUME = 18,
+ PAGES = {292-298},
+ PDF = {zhang2003.tree.pdf},
+ DOI = {10.1016/S0169-5347(03)00033-8},
+ PMID = {},
+ KEYWORDS = {gene duplication}
+ }
+
+ at ARTICLE{zhang2003a,
+ AUTHOR = {Zhang, Yu and Waterman, Michael S.},
+ YEAR = 2003,
+ TITLE = {An {Eulerian} Path Approach to Global Multiple Alignment for {DNA} Sequences},
+ JOURNAL = {J. Comput. Biol.},
+ VOLUME = 10,
+ PAGES = {803-819},
+ PDF = {zhang2003a.jcb.pdf},
+ DOI = {10.1089/106652703322756096},
+ PMID = {},
+ KEYWORDS = {multiple sequence alignment; de Bruijn graph; Eulerian path}
+ }
+
+ at ARTICLE{zhang2004,
+ AUTHOR = {Zhang, Jianzhi},
+ YEAR = 2004,
+ TITLE = {Frequent False Detection of Positive Selection by the Likelihood Method with Branch-Site Models},
+ JOURNAL = {Mol. Biol. Evol.},
+ VOLUME = 21,
+ PAGES = {1332-1339},
+ PDF = {zhang2004.mbe.pdf},
+ DOI = {10.1093/molbev/msh117},
+ PMID = {15014150},
+ KEYWORDS = {likelihood; computer simulation; positive selection; branch-site model; molecular evolution}
+ }
+
+ at ARTICLE{zhang2003,
+ AUTHOR = {Zhang, Li and Tang, Chun and Song, Yuqing and Zhang, Aidong and Ramanathan, Murali},
+ YEAR = 2003,
+ TITLE = {VizCluster and its Application on Classifying Gene Expression Data},
+ JOURNAL = {Distributed and Parallel Databases},
+ VOLUME = 13,
+ PAGES = {73-97},
+ PDF = {zhang2003.dpdb.pdf},
+ DOI = {10.1023/A:1021517806825},
+ PMID = {},
+ KEYWORDS = {parallel computing; parallel bioinformatics;; interactive visualization; gene expression; classification}
+ }
+
+ at ARTICLE{zhang2003,
+ AUTHOR = {Zhang, Aidong},
+ YEAR = 2003,
+ TITLE = {Introduction to the Special Issue on Bioinformatics},
+ JOURNAL = {Distributed and Parallel Databases},
+ VOLUME = 13,
+ PAGES = {5-6},
+ PDF = {zhang2003a.dpdb.pdf},
+ DOI = {10.1023/A:1021521924089},
+ PMID = {},
+ KEYWORDS = {parallel computing; parallel bioinformatics; parallel databases;; }
+ }
+
+ at ARTICLE{zhao1998,
+ AUTHOR = {Zhao, Zhongming and Hewett-Emmett, David and Li, Wen-Hsiung},
+ YEAR = 1998,
+ TITLE = {Frequent Gene Conversion Between Human Red and Green Opsin Genes},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 46,
+ PAGES = {494-496},
+ PDF = {zhao1998.jme.pdf},
+ DOI = {},
+ PMID = {9541545},
+ KEYWORDS = {red and green opsin genes; gene conversion; natural selection; introns; exons}
+ }
+
+ at ARTICLE{zharkikh1994,
+ AUTHOR = {Zharkikh, Andrey},
+ YEAR = 1994,
+ TITLE = {Estimation of Evolutionary Distances Between Nucleotide Sequences},
+ JOURNAL = {J. Mol. Evol.},
+ VOLUME = 39,
+ PAGES = {315-329},
+ PDF = {hardcopy},
+ DOI = {},
+ PMID = {7932793},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{zhou2003,
+ AUTHOR = {Zhou, B. B. and Brent, R. P.},
+ YEAR = 2003,
+ TITLE = {An efficient method for computing eigenvalues of a real normal matrix},
+ JOURNAL = {J. Parallel Distrib. Comput.},
+ VOLUME = 63,
+ PAGES = {638-648},
+ PDF = {zhou2003.jpdc.pdf},
+ DOI = {10.1016/S0743-7315(03)00007-8},
+ PMID = {},
+ KEYWORDS = {parallel computing; Eigenvalue decomposition; Normal matrix; Jacobi algorithm and QR algorithm; Parallel computing}
+ }
+
+ at ARTICLE{zillig1991,
+ AUTHOR = {Zillig, Wolfgang},
+ YEAR = 1991,
+ TITLE = {Comparative biochemistry of {Archaea} and {Bacteria}},
+ JOURNAL = {Curr. Opin. Genet. Dev.},
+ VOLUME = 1,
+ PAGES = {544-551},
+ PDF = {hardcopy},
+ PDF-TODO = {zillig1991.curr-opin-genet-dev.pdf},
+ DOI = {},
+ PMID = {1822288},
+ KEYWORDS = {network-like evolution of the three domains of life}
+ }
+
+ at ARTICLE{zimmerman1982,
+ AUTHOR = {Zimmerman, Steven B.},
+ YEAR = 1982,
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+ PDF = {hardcopy},
+ DOI = {},
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+
+ at ARTICLE{zoellner2000,
+ AUTHOR = {Z\"{o}llner, Sebastian and von Haeseler, Arndt},
+ YEAR = 2000,
+ TITLE = {A Coalescent Approach to Study Linkage Disequilibrium between Single-Nucleotide Polymorphisms},
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+ VOLUME = 66,
+ PAGES = {615-628},
+ PDF = {zoellner2000.am-j-hum-genet.pdf},
+ DOI = {},
+ PMID = {10677321},
+ KEYWORDS = {}
+ }
+
+ at ARTICLE{zoller2003,
+ AUTHOR = {Zoller, Stefan and Lutzoni, Fran\c{c}ois},
+ YEAR = 2003,
+ TITLE = {Slow algae, fast fungi: exceptionally high nucleotide substitution rate differences between lichenized fungi {Omphalina} and their symbiotic green algae {Coccomyxa}},
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+ VOLUME = 29,
+ PAGES = {629-640},
+ PDF = {zoller2003.mpe.pdf},
+ DOI = {10.1016/S1055-7903(03)00215-X},
+ PMID = {},
+ KEYWORDS = {Nucleotide substitution rates; Coevolution; Mutualistic symbiosis; Lichens; Inhabitant/exhabitant; Basidiomycota; Omphalina; Coccomyxa}
+ }
+
+ at ARTICLE{zwickl2002,
+ AUTHOR = {Zwickl, Derrick J. and Hillis, David M.},
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+ PAGES = {588-598},
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+ DOI = {10.1080/10635150290102339},
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+ KEYWORDS = {Phylogenetic accuracy; phylogenetic error; taxon sampling}
+ }
+
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