[med-svn] [paml] branch master updated (a1cb73a -> a4c5795)
Andreas Tille
tille at debian.org
Tue May 3 12:02:32 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository paml.
from a1cb73a Moved packaging to git
new 201566e Use new uscan options in watch file
new ef9c81c Imported Upstream version 4.9a+dfsg
new b23918d Merge tag 'upstream/4.9a+dfsg'
new 0b69157 New upstream version
new 6ba7379 Author confirmed GPL license at https://groups.google.com/forum/#!topic/pamlsoftware/NFu_lNBoAEA
new e15e953 cme fix dpkg-control
new 5ed92be Remove *.pdf files without source
new beb5829 Imported Upstream version 4.91+dfsg
new 598814a Merge tag 'upstream/4.91+dfsg'
new 63834ec Removed *.pdf files since there is no source for theses files
new 66ea750 Refresh patches
new 942d163 Fix install
new 59f5d7a Doc is also in main
new 007b3bd Link to online docs
new 522fa5d Add clean target to upstream Makefile
new 9cc70c5 Fix typo
new 7bcf97a Install more data
new fcae1ec Provide control files and point these correctly to the according data files
new a4c5795 Make sure *.ctl files point to the correct location and existing data files
The 19 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
MCbase.dat | 4 +-
MCbaseRandomTree.dat | 4 +-
Technical/Pt/eigenQREV.pdf | Bin 146138 -> 0 bytes
Technical/Pt/testPMat.c | 0
Technical/Simulation/Codon/MCcodonNSbranches.dat | 0
.../Simulation/Codon/MCcodonNSbranchsites.dat | 0
Technical/Simulation/Codon/MCcodonNSsites.dat | 0
Technical/Simulation/Codon/PositiveSites.c | 0
Technical/Simulation/Codon/README.txt | 0
Technical/Simulation/Codon/codeml.ctl | 120 +-
Technical/Simulation/multiruns.c | 0
Technical/Simulation/multiruns.txt | 0
aaml.ctl | 72 +-
codonml.ctl | 104 +-
dat/MtZoa.dat | 0
dat/cpREV10.dat | 0
dat/cpREV64.dat | 56 +-
dat/dayhoff-dcmut.dat | 0
dat/dayhoff.dat | 0
dat/g1974a.dat | 0
dat/g1974c.dat | 0
dat/g1974p.dat | 0
dat/g1974v.dat | 0
dat/grantham.dat | 0
dat/jones-dcmut.dat | 0
dat/jones.dat | 0
dat/lg.dat | 0
dat/miyata.dat | 0
dat/mtArt.dat | 0
dat/mtREV24.dat | 0
dat/mtmam.dat | 156 +-
dat/wag.dat | 0
debian/README.source | 8 +-
debian/changelog | 9 +-
debian/control | 18 +-
debian/copyright | 29 +-
debian/paml-doc.README.Debian | 17 +
debian/{README.Debian => paml.README.Debian} | 2 +-
debian/paml.docs | 3 +-
debian/paml.install | 28 +-
debian/paml.links | 9 +
debian/patches/add_clean_target.patch | 14 +
debian/patches/fix_format_security.patch | 13 +-
debian/patches/hardening.patch | 14 +-
debian/patches/makefile.patch | 30 -
debian/patches/series | 2 +-
debian/rules | 28 +-
debian/watch | 2 +-
doc/MCMCtreeDOC.pdf | Bin 291668 -> 0 bytes
doc/pamlDOC.pdf | Bin 646805 -> 0 bytes
doc/pamlFAQs.pdf | Bin 179912 -> 0 bytes
doc/pamlHistory.txt | 105 +-
examples/CladeModelCD/CladeModelCnotes.doc | Bin 109568 -> 0 bytes
examples/CladeModelCD/CladeModelCnotes.pdf | Bin 45327 -> 0 bytes
examples/CladeModelCD/Dataset1.CladeC/rooted.pdf | Bin 12134 -> 0 bytes
examples/CladeModelCD/Dataset1.CladeC/tree.txt | 2 -
.../CladeModelCD/Dataset2.CladeD/ECP_EDN_17.nuc | 189 -
examples/CladeModelCD/Dataset2.CladeD/tree.txt | 2 -
examples/CladeModelCD/Dataset2.CladeD/unrooted.pdf | Bin 12239 -> 0 bytes
.../{Dataset1.CladeC => }/ECP_EDN_15.nuc | 0
.../codeml.ctl => codeml.CladeC.ctl} | 11 +-
.../codeml.ctl => codeml.CladeD.ctl} | 4 +-
examples/CladeModelCD/tree.txt | 4 +
examples/DatingSoftBound/FigTree.tre | 6 -
examples/DatingSoftBound/FixedDsClock23.txt | 8 +
.../DatingSoftBound/mcmctree.Infinitesites.ctl | 2 +-
examples/DatingSoftBound/mcmctree.ctl | 4 +-
examples/HIVNSsites/HIVenvSweden.trees | 0
examples/HIVNSsites/HIVenvSweden.txt | 0
examples/HIVNSsites/HIVenvSweden4s.trees | 0
examples/HIVNSsites/HIVenvSweden4s.txt | 0
examples/HIVNSsites/README.txt | 0
examples/HIVNSsites/codeml.ctl | 0
examples/MHC.Swanson2002MBE/README.txt | 0
examples/MHC.Swanson2002MBE/bigmhc.phy | 0
examples/MHC.Swanson2002MBE/bigmhc.trees | 6 +-
examples/MHC.Swanson2002MBE/codeml.ctl | 66 +-
examples/MouseLemurs/MouseLemurs.aa | 0
examples/MouseLemurs/MouseLemurs.nuc | 0
examples/MouseLemurs/MouseLemurs.trees | 0
examples/MouseLemurs/MouseLemurs123.nuc | 0
examples/MouseLemurs/README.txt | 0
examples/MouseLemurs/README2.txt | 0
examples/MouseLemurs/aaml.ctl | 0
examples/MouseLemurs/aaml2.ctl | 0
examples/MouseLemurs/baseml.ctl | 0
examples/MouseLemurs/baseml2.ctl | 0
examples/MouseLemurs/codeml.ctl | 0
examples/MouseLemurs/codonml.ctl | 0
examples/MouseLemurs/codonml2.ctl | 0
examples/MouseLemurs/mtmam.dat | 0
examples/TipDate.FluH1/H1.Beast.Nulldata.xml | 0
examples/TipDate.FluH1/H1.Beast.xml | 0
examples/TipDate.FluH1/H1.NodeNumbers.tre | 8 +-
examples/TipDate.FluH1/H1.nexus | 0
examples/TipDate.FluH1/H1.tre | 0
examples/TipDate.FluH1/H1.txt | 0
examples/TipDate.FluH1/SeedUsed | 1 -
examples/TipDate.FluH1/baseml.ctl | 0
examples/TipDate.FluH1/commands.txt | 0
examples/TipDate.FluH1/in.BV.HKYG5 | 1174 +-
examples/TipDate.FluH1/mcmctreeClock1.ctl | 0
examples/TipDate.FluH1/mcmctreeClock2.ctl | 0
examples/TipDate.FluH1/mcmctreeClock3.ctl | 0
examples/TipDate.HIV2/HIV2ge.tre | 0
examples/TipDate.HIV2/HIV2ge.txt | 0
examples/TipDate.HIV2/README.txt | 0
examples/TipDate.HIV2/baseml.ctl | 0
examples/TipDate.HIV2/in.BV.HKYG5 | 0
examples/TipDate.HIV2/mcmctree.ExactlnL.ctl | 0
examples/TipDate.HIV2/mcmctree.ctl | 0
examples/lysin/README.txt | 0
examples/lysin/RasMol.txt | 0
examples/lysin/SiteNumbering.txt | 0
examples/lysin/codeml.ctl | 0
examples/lysin/codemlYangSwanson2002.ctl | 0
examples/lysin/lysin.nuc | 0
examples/lysin/lysin.trees | 0
examples/lysin/lysinYangSwanson2002.nuc | 0
examples/lysozyme/README.txt | 0
examples/lysozyme/codeml.ctl | 0
examples/lysozyme/lysozymeLarge.ctl | 0
examples/lysozyme/lysozymeLarge.nuc | 0
examples/lysozyme/lysozymeLarge.trees | 0
examples/lysozyme/lysozymeSmall.ctl | 0
examples/lysozyme/lysozymeSmall.nuc | 0
examples/lysozyme/lysozymeSmall.trees | 0
examples/lysozyme/lysozymeSmall.txt | 0
examples/mtCDNA/README.txt | 0
examples/mtCDNA/codeml.ctl | 0
examples/mtCDNA/miyata.dat | 0
examples/mtCDNA/mtCDNAmam.nuc | 0
examples/mtCDNA/mtCDNAmam.trees | 0
examples/mtCDNA/mtCDNApri.aa | 0
examples/mtCDNA/mtCDNApri.nuc | 0
examples/mtCDNA/mtCDNApri.trees | 0
examples/mtCDNAape/2s.trees | 0
examples/mtCDNAape/OmegaAA.dat | 0
examples/mtCDNAape/README.txt | 10 +-
examples/mtCDNAape/codeml.HC.ctl | 2 +-
examples/mtCDNAape/codeml.ctl | 0
examples/mtCDNAape/mtCDNA.HC.txt | 0
examples/mtCDNAape/mtCDNAape.trees | 0
examples/mtCDNAape/mtCDNAape.txt | 0
mcmctree.ctl | 2 +-
src/Makefile | 13 +-
src/README.txt | 8 +
src/baseml.c | 144 +-
src/basemlg.c | 15 +-
src/codeml.c | 17 +-
src/evolver.c | 403 +-
src/mcmctree.c | 893 +-
src/paml.h | 72 +-
src/tools.c | 386 +-
src/treespace.c | 16 +-
src/treesub.c | 16334 ++++++++++---------
156 files changed, 10587 insertions(+), 10062 deletions(-)
delete mode 100755 Technical/Pt/eigenQREV.pdf
mode change 100755 => 100644 Technical/Pt/testPMat.c
mode change 100755 => 100644 Technical/Simulation/Codon/MCcodonNSbranches.dat
mode change 100755 => 100644 Technical/Simulation/Codon/MCcodonNSbranchsites.dat
mode change 100755 => 100644 Technical/Simulation/Codon/MCcodonNSsites.dat
mode change 100755 => 100644 Technical/Simulation/Codon/PositiveSites.c
mode change 100755 => 100644 Technical/Simulation/Codon/README.txt
mode change 100755 => 100644 Technical/Simulation/Codon/codeml.ctl
mode change 100755 => 100644 Technical/Simulation/multiruns.c
mode change 100755 => 100644 Technical/Simulation/multiruns.txt
mode change 100755 => 100644 dat/MtZoa.dat
mode change 100755 => 100644 dat/cpREV10.dat
mode change 100755 => 100644 dat/cpREV64.dat
mode change 100755 => 100644 dat/dayhoff-dcmut.dat
mode change 100755 => 100644 dat/dayhoff.dat
mode change 100755 => 100644 dat/g1974a.dat
mode change 100755 => 100644 dat/g1974c.dat
mode change 100755 => 100644 dat/g1974p.dat
mode change 100755 => 100644 dat/g1974v.dat
mode change 100755 => 100644 dat/grantham.dat
mode change 100755 => 100644 dat/jones-dcmut.dat
mode change 100755 => 100644 dat/jones.dat
mode change 100755 => 100644 dat/lg.dat
mode change 100755 => 100644 dat/miyata.dat
mode change 100755 => 100644 dat/mtArt.dat
mode change 100755 => 100644 dat/mtREV24.dat
mode change 100755 => 100644 dat/mtmam.dat
mode change 100755 => 100644 dat/wag.dat
create mode 100644 debian/paml-doc.README.Debian
rename debian/{README.Debian => paml.README.Debian} (92%)
create mode 100644 debian/patches/add_clean_target.patch
delete mode 100644 debian/patches/makefile.patch
delete mode 100644 doc/MCMCtreeDOC.pdf
delete mode 100644 doc/pamlDOC.pdf
delete mode 100644 doc/pamlFAQs.pdf
delete mode 100644 examples/CladeModelCD/CladeModelCnotes.doc
delete mode 100644 examples/CladeModelCD/CladeModelCnotes.pdf
delete mode 100755 examples/CladeModelCD/Dataset1.CladeC/rooted.pdf
delete mode 100755 examples/CladeModelCD/Dataset1.CladeC/tree.txt
delete mode 100755 examples/CladeModelCD/Dataset2.CladeD/ECP_EDN_17.nuc
delete mode 100755 examples/CladeModelCD/Dataset2.CladeD/tree.txt
delete mode 100755 examples/CladeModelCD/Dataset2.CladeD/unrooted.pdf
rename examples/CladeModelCD/{Dataset1.CladeC => }/ECP_EDN_15.nuc (100%)
mode change 100755 => 100644
rename examples/CladeModelCD/{Dataset2.CladeD/codeml.ctl => codeml.CladeC.ctl} (81%)
mode change 100755 => 100644
rename examples/CladeModelCD/{Dataset1.CladeC/codeml.ctl => codeml.CladeD.ctl} (89%)
mode change 100755 => 100644
create mode 100644 examples/CladeModelCD/tree.txt
delete mode 100644 examples/DatingSoftBound/FigTree.tre
mode change 100755 => 100644 examples/HIVNSsites/HIVenvSweden.trees
mode change 100755 => 100644 examples/HIVNSsites/HIVenvSweden.txt
mode change 100755 => 100644 examples/HIVNSsites/HIVenvSweden4s.trees
mode change 100755 => 100644 examples/HIVNSsites/HIVenvSweden4s.txt
mode change 100755 => 100644 examples/HIVNSsites/README.txt
mode change 100755 => 100644 examples/HIVNSsites/codeml.ctl
mode change 100755 => 100644 examples/MHC.Swanson2002MBE/README.txt
mode change 100755 => 100644 examples/MHC.Swanson2002MBE/bigmhc.phy
mode change 100755 => 100644 examples/MHC.Swanson2002MBE/bigmhc.trees
mode change 100755 => 100644 examples/MHC.Swanson2002MBE/codeml.ctl
mode change 100755 => 100644 examples/MouseLemurs/MouseLemurs.aa
mode change 100755 => 100644 examples/MouseLemurs/MouseLemurs.nuc
mode change 100755 => 100644 examples/MouseLemurs/MouseLemurs.trees
mode change 100755 => 100644 examples/MouseLemurs/MouseLemurs123.nuc
mode change 100755 => 100644 examples/MouseLemurs/README.txt
mode change 100755 => 100644 examples/MouseLemurs/README2.txt
mode change 100755 => 100644 examples/MouseLemurs/aaml.ctl
mode change 100755 => 100644 examples/MouseLemurs/aaml2.ctl
mode change 100755 => 100644 examples/MouseLemurs/baseml.ctl
mode change 100755 => 100644 examples/MouseLemurs/baseml2.ctl
mode change 100755 => 100644 examples/MouseLemurs/codeml.ctl
mode change 100755 => 100644 examples/MouseLemurs/codonml.ctl
mode change 100755 => 100644 examples/MouseLemurs/codonml2.ctl
mode change 100755 => 100644 examples/MouseLemurs/mtmam.dat
mode change 100755 => 100644 examples/TipDate.FluH1/H1.Beast.Nulldata.xml
mode change 100755 => 100644 examples/TipDate.FluH1/H1.Beast.xml
mode change 100755 => 100644 examples/TipDate.FluH1/H1.NodeNumbers.tre
mode change 100755 => 100644 examples/TipDate.FluH1/H1.nexus
mode change 100755 => 100644 examples/TipDate.FluH1/H1.tre
mode change 100755 => 100644 examples/TipDate.FluH1/H1.txt
delete mode 100755 examples/TipDate.FluH1/SeedUsed
mode change 100755 => 100644 examples/TipDate.FluH1/baseml.ctl
mode change 100755 => 100644 examples/TipDate.FluH1/commands.txt
mode change 100755 => 100644 examples/TipDate.FluH1/in.BV.HKYG5
mode change 100755 => 100644 examples/TipDate.FluH1/mcmctreeClock1.ctl
mode change 100755 => 100644 examples/TipDate.FluH1/mcmctreeClock2.ctl
mode change 100755 => 100644 examples/TipDate.FluH1/mcmctreeClock3.ctl
mode change 100755 => 100644 examples/TipDate.HIV2/HIV2ge.tre
mode change 100755 => 100644 examples/TipDate.HIV2/HIV2ge.txt
mode change 100755 => 100644 examples/TipDate.HIV2/README.txt
mode change 100755 => 100644 examples/TipDate.HIV2/baseml.ctl
mode change 100755 => 100644 examples/TipDate.HIV2/in.BV.HKYG5
mode change 100755 => 100644 examples/TipDate.HIV2/mcmctree.ExactlnL.ctl
mode change 100755 => 100644 examples/TipDate.HIV2/mcmctree.ctl
mode change 100755 => 100644 examples/lysin/README.txt
mode change 100755 => 100644 examples/lysin/RasMol.txt
mode change 100755 => 100644 examples/lysin/SiteNumbering.txt
mode change 100755 => 100644 examples/lysin/codeml.ctl
mode change 100755 => 100644 examples/lysin/codemlYangSwanson2002.ctl
mode change 100755 => 100644 examples/lysin/lysin.nuc
mode change 100755 => 100644 examples/lysin/lysin.trees
mode change 100755 => 100644 examples/lysin/lysinYangSwanson2002.nuc
mode change 100755 => 100644 examples/lysozyme/README.txt
mode change 100755 => 100644 examples/lysozyme/codeml.ctl
mode change 100755 => 100644 examples/lysozyme/lysozymeLarge.ctl
mode change 100755 => 100644 examples/lysozyme/lysozymeLarge.nuc
mode change 100755 => 100644 examples/lysozyme/lysozymeLarge.trees
mode change 100755 => 100644 examples/lysozyme/lysozymeSmall.ctl
mode change 100755 => 100644 examples/lysozyme/lysozymeSmall.nuc
mode change 100755 => 100644 examples/lysozyme/lysozymeSmall.trees
mode change 100755 => 100644 examples/lysozyme/lysozymeSmall.txt
mode change 100755 => 100644 examples/mtCDNA/README.txt
mode change 100755 => 100644 examples/mtCDNA/codeml.ctl
mode change 100755 => 100644 examples/mtCDNA/miyata.dat
mode change 100755 => 100644 examples/mtCDNA/mtCDNAmam.nuc
mode change 100755 => 100644 examples/mtCDNA/mtCDNAmam.trees
mode change 100755 => 100644 examples/mtCDNA/mtCDNApri.aa
mode change 100755 => 100644 examples/mtCDNA/mtCDNApri.nuc
mode change 100755 => 100644 examples/mtCDNA/mtCDNApri.trees
mode change 100755 => 100644 examples/mtCDNAape/2s.trees
mode change 100755 => 100644 examples/mtCDNAape/OmegaAA.dat
mode change 100755 => 100644 examples/mtCDNAape/README.txt
mode change 100755 => 100644 examples/mtCDNAape/codeml.HC.ctl
mode change 100755 => 100644 examples/mtCDNAape/codeml.ctl
mode change 100755 => 100644 examples/mtCDNAape/mtCDNA.HC.txt
mode change 100755 => 100644 examples/mtCDNAape/mtCDNAape.trees
mode change 100755 => 100644 examples/mtCDNAape/mtCDNAape.txt
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