[med-svn] [muscle] branch upstream updated (3b7bc21 -> 0d81e90)
Andreas Tille
tille at debian.org
Mon Jan 18 16:11:32 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository muscle.
from 3b7bc21 Imported Upstream version 3.8.31
new 0d81e90 Imported Upstream version 3.8.31+dfsg
The 1 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:
muscle.vcproj | 922 -----------------------
muscle21.vcproj | 423 -----------
Makefile => src/Makefile | 0
README.txt => src/README.txt | 0
aligngivenpath.cpp => src/aligngivenpath.cpp | 0
aligngivenpathsw.cpp => src/aligngivenpathsw.cpp | 0
aligntwomsas.cpp => src/aligntwomsas.cpp | 0
aligntwoprofs.cpp => src/aligntwoprofs.cpp | 0
aln.cpp => src/aln.cpp | 0
alpha.cpp => src/alpha.cpp | 0
alpha.h => src/alpha.h | 0
anchors.cpp => src/anchors.cpp | 0
bittraceback.cpp => src/bittraceback.cpp | 0
blosum62.cpp => src/blosum62.cpp | 0
blosumla.cpp => src/blosumla.cpp | 0
clust.cpp => src/clust.cpp | 0
clust.h => src/clust.h | 0
cluster.cpp => src/cluster.cpp | 0
cluster.h => src/cluster.h | 0
clustset.h => src/clustset.h | 0
clustsetdf.h => src/clustsetdf.h | 0
clustsetmsa.h => src/clustsetmsa.h | 0
clwwt.cpp => src/clwwt.cpp | 0
color.cpp => src/color.cpp | 0
cons.cpp => src/cons.cpp | 0
diaglist.cpp => src/diaglist.cpp | 0
diaglist.h => src/diaglist.h | 0
diffobjscore.cpp => src/diffobjscore.cpp | 0
diffpaths.cpp => src/diffpaths.cpp | 0
difftrees.cpp => src/difftrees.cpp | 0
difftreese.cpp => src/difftreese.cpp | 0
distcalc.cpp => src/distcalc.cpp | 0
distcalc.h => src/distcalc.h | 0
distfunc.cpp => src/distfunc.cpp | 0
distfunc.h => src/distfunc.h | 0
distpwkimura.cpp => src/distpwkimura.cpp | 0
domuscle.cpp => src/domuscle.cpp | 0
dosp.cpp => src/dosp.cpp | 0
dpregionlist.h => src/dpregionlist.h | 0
dpreglist.cpp => src/dpreglist.cpp | 0
dpreglist.h => src/dpreglist.h | 0
drawtree.cpp => src/drawtree.cpp | 0
edgelist.cpp => src/edgelist.cpp | 0
edgelist.h => src/edgelist.h | 0
enumopts.cpp => src/enumopts.cpp | 0
enumopts.h => src/enumopts.h | 0
enums.h => src/enums.h | 0
enumtostr.cpp => src/enumtostr.cpp | 0
estring.cpp => src/estring.cpp | 0
estring.h => src/estring.h | 0
fasta.cpp => src/fasta.cpp | 0
fasta2.cpp => src/fasta2.cpp | 0
fastclust.cpp => src/fastclust.cpp | 0
fastdist.cpp => src/fastdist.cpp | 0
fastdistjones.cpp => src/fastdistjones.cpp | 0
fastdistkbit.cpp => src/fastdistkbit.cpp | 0
fastdistkmer.cpp => src/fastdistkmer.cpp | 0
fastdistmafft.cpp => src/fastdistmafft.cpp | 0
fastdistnuc.cpp => src/fastdistnuc.cpp | 0
fastscorepath2.cpp => src/fastscorepath2.cpp | 0
finddiags.cpp => src/finddiags.cpp | 0
finddiagsn.cpp => src/finddiagsn.cpp | 0
gapscoredimer.h => src/gapscoredimer.h | 0
gatest.cpp => src/gatest.cpp | 0
glbalign.cpp => src/glbalign.cpp | 0
glbalign352.cpp => src/glbalign352.cpp | 0
glbaligndiag.cpp => src/glbaligndiag.cpp | 0
glbalignla.cpp => src/glbalignla.cpp | 0
glbalignle.cpp => src/glbalignle.cpp | 0
glbalignns.cpp => src/glbalignns.cpp | 0
glbalignsimple.cpp => src/glbalignsimple.cpp | 0
glbalignsp.cpp => src/glbalignsp.cpp | 0
glbalignspn.cpp => src/glbalignspn.cpp | 0
glbalignss.cpp => src/glbalignss.cpp | 0
glbalndimer.cpp => src/glbalndimer.cpp | 0
globals.cpp => src/globals.cpp | 0
globalslinux.cpp => src/globalslinux.cpp | 0
globalsosx.cpp => src/globalsosx.cpp | 0
globalsother.cpp => src/globalsother.cpp | 0
globalswin32.cpp => src/globalswin32.cpp | 0
gonnet.cpp => src/gonnet.cpp | 0
gonnet.h => src/gonnet.h | 0
gotowt.cpp => src/gotowt.cpp | 0
henikoffweight.cpp => src/henikoffweight.cpp | 0
henikoffweightpb.cpp => src/henikoffweightpb.cpp | 0
html.cpp => src/html.cpp | 0
hydro.cpp => src/hydro.cpp | 0
intmath.cpp => src/intmath.cpp | 0
intmath.h => src/intmath.h | 0
local.cpp => src/local.cpp | 0
main.cpp => src/main.cpp | 0
make.err => src/make.err | 0
make.out => src/make.out | 0
makerootmsa.cpp => src/makerootmsa.cpp | 0
makerootmsab.cpp => src/makerootmsab.cpp | 0
maketree.cpp => src/maketree.cpp | 0
mhack.cpp => src/mhack.cpp | 0
mk => src/mk | 0
mpam200.cpp => src/mpam200.cpp | 0
msa.cpp => src/msa.cpp | 0
msa.h => src/msa.h | 0
msa2.cpp => src/msa2.cpp | 0
msadist.h => src/msadist.h | 0
msadistkimura.cpp => src/msadistkimura.cpp | 0
msadistkimura.h => src/msadistkimura.h | 0
msadistmafft.h => src/msadistmafft.h | 0
msf.cpp => src/msf.cpp | 0
muscle.cpp => src/muscle.cpp | 0
muscle.h => src/muscle.h | 0
muscleout.cpp => src/muscleout.cpp | 0
nucmx.cpp => src/nucmx.cpp | 0
nwdasimple.cpp => src/nwdasimple.cpp | 0
nwdasimple2.cpp => src/nwdasimple2.cpp | 0
nwdasmall.cpp => src/nwdasmall.cpp | 0
nwrec.cpp => src/nwrec.cpp | 0
nwsmall.cpp => src/nwsmall.cpp | 0
objscore.cpp => src/objscore.cpp | 0
objscore.h => src/objscore.h | 0
objscore2.cpp => src/objscore2.cpp | 0
objscoreda.cpp => src/objscoreda.cpp | 0
onexception.cpp => src/onexception.cpp | 0
options.cpp => src/options.cpp | 0
outweights.cpp => src/outweights.cpp | 0
pam200mafft.cpp => src/pam200mafft.cpp | 0
params.cpp => src/params.cpp | 0
params.h => src/params.h | 0
phy.cpp => src/phy.cpp | 0
phy2.cpp => src/phy2.cpp | 0
phy3.cpp => src/phy3.cpp | 0
phy4.cpp => src/phy4.cpp | 0
phyfromclust.cpp => src/phyfromclust.cpp | 0
phyfromfile.cpp => src/phyfromfile.cpp | 0
physeq.cpp => src/physeq.cpp | 0
phytofile.cpp => src/phytofile.cpp | 0
posgap.cpp => src/posgap.cpp | 0
ppscore.cpp => src/ppscore.cpp | 0
profdb.cpp => src/profdb.cpp | 0
profile.cpp => src/profile.cpp | 0
profile.h => src/profile.h | 0
profilefrommsa.cpp => src/profilefrommsa.cpp | 0
progalign.cpp => src/progalign.cpp | 0
progress.cpp => src/progress.cpp | 0
progressivealign.cpp => src/progressivealign.cpp | 0
pwpath.cpp => src/pwpath.cpp | 0
pwpath.h => src/pwpath.h | 0
readmx.cpp => src/readmx.cpp | 0
realigndiffs.cpp => src/realigndiffs.cpp | 0
realigndiffse.cpp => src/realigndiffse.cpp | 0
redblack.cpp => src/redblack.cpp | 0
refine.cpp => src/refine.cpp | 0
refinehoriz.cpp => src/refinehoriz.cpp | 0
refinesubfams.cpp => src/refinesubfams.cpp | 0
refinetree.cpp => src/refinetree.cpp | 0
refinetreee.cpp => src/refinetreee.cpp | 0
refinevert.cpp => src/refinevert.cpp | 0
refinew.cpp => src/refinew.cpp | 0
releases.txt => src/releases.txt | 0
savebest.cpp => src/savebest.cpp | 0
scoredist.cpp => src/scoredist.cpp | 0
scoregaps.cpp => src/scoregaps.cpp | 0
scorehistory.cpp => src/scorehistory.cpp | 0
scorehistory.h => src/scorehistory.h | 0
scoremx.cpp => src/scoremx.cpp | 0
scorepp.cpp => src/scorepp.cpp | 0
seq.cpp => src/seq.cpp | 0
seq.h => src/seq.h | 0
seqvect.cpp => src/seqvect.cpp | 0
seqvect.h => src/seqvect.h | 0
setblosumweights.cpp => src/setblosumweights.cpp | 0
setgscweights.cpp => src/setgscweights.cpp | 0
setnewhandler.cpp => src/setnewhandler.cpp | 0
spfast.cpp => src/spfast.cpp | 0
sptest.cpp => src/sptest.cpp | 0
stabilize.cpp => src/stabilize.cpp | 0
subfam.cpp => src/subfam.cpp | 0
subfams.cpp => src/subfams.cpp | 0
svnmods.h => src/svnmods.h | 0
svnversion.h => src/svnversion.h | 0
sw.cpp => src/sw.cpp | 0
termgaps.cpp => src/termgaps.cpp | 0
textfile.cpp => src/textfile.cpp | 0
textfile.h => src/textfile.h | 0
threewaywt.cpp => src/threewaywt.cpp | 0
timing.h => src/timing.h | 0
tomhydro.cpp => src/tomhydro.cpp | 0
traceback.cpp => src/traceback.cpp | 0
tracebackopt.cpp => src/tracebackopt.cpp | 0
tracebacksw.cpp => src/tracebacksw.cpp | 0
tree.h => src/tree.h | 0
treefrommsa.cpp => src/treefrommsa.cpp | 0
types.h => src/types.h | 0
typetostr.cpp => src/typetostr.cpp | 0
unixio.h => src/unixio.h | 0
upgma2.cpp => src/upgma2.cpp | 0
usage.cpp => src/usage.cpp | 0
validateids.cpp => src/validateids.cpp | 0
version.txt => src/version.txt | 0
vtml2.cpp => src/vtml2.cpp | 0
writescorefile.cpp => src/writescorefile.cpp | 0
199 files changed, 1345 deletions(-)
delete mode 100644 muscle.vcproj
delete mode 100644 muscle21.vcproj
rename Makefile => src/Makefile (100%)
rename README.txt => src/README.txt (100%)
rename aligngivenpath.cpp => src/aligngivenpath.cpp (100%)
rename aligngivenpathsw.cpp => src/aligngivenpathsw.cpp (100%)
rename aligntwomsas.cpp => src/aligntwomsas.cpp (100%)
rename aligntwoprofs.cpp => src/aligntwoprofs.cpp (100%)
rename aln.cpp => src/aln.cpp (100%)
rename alpha.cpp => src/alpha.cpp (100%)
rename alpha.h => src/alpha.h (100%)
rename anchors.cpp => src/anchors.cpp (100%)
rename bittraceback.cpp => src/bittraceback.cpp (100%)
rename blosum62.cpp => src/blosum62.cpp (100%)
rename blosumla.cpp => src/blosumla.cpp (100%)
rename clust.cpp => src/clust.cpp (100%)
rename clust.h => src/clust.h (100%)
rename cluster.cpp => src/cluster.cpp (100%)
rename cluster.h => src/cluster.h (100%)
rename clustset.h => src/clustset.h (100%)
rename clustsetdf.h => src/clustsetdf.h (100%)
rename clustsetmsa.h => src/clustsetmsa.h (100%)
rename clwwt.cpp => src/clwwt.cpp (100%)
rename color.cpp => src/color.cpp (100%)
rename cons.cpp => src/cons.cpp (100%)
rename diaglist.cpp => src/diaglist.cpp (100%)
rename diaglist.h => src/diaglist.h (100%)
rename diffobjscore.cpp => src/diffobjscore.cpp (100%)
rename diffpaths.cpp => src/diffpaths.cpp (100%)
rename difftrees.cpp => src/difftrees.cpp (100%)
rename difftreese.cpp => src/difftreese.cpp (100%)
rename distcalc.cpp => src/distcalc.cpp (100%)
rename distcalc.h => src/distcalc.h (100%)
rename distfunc.cpp => src/distfunc.cpp (100%)
rename distfunc.h => src/distfunc.h (100%)
rename distpwkimura.cpp => src/distpwkimura.cpp (100%)
rename domuscle.cpp => src/domuscle.cpp (100%)
rename dosp.cpp => src/dosp.cpp (100%)
rename dpregionlist.h => src/dpregionlist.h (100%)
rename dpreglist.cpp => src/dpreglist.cpp (100%)
rename dpreglist.h => src/dpreglist.h (100%)
rename drawtree.cpp => src/drawtree.cpp (100%)
rename edgelist.cpp => src/edgelist.cpp (100%)
rename edgelist.h => src/edgelist.h (100%)
rename enumopts.cpp => src/enumopts.cpp (100%)
rename enumopts.h => src/enumopts.h (100%)
rename enums.h => src/enums.h (100%)
rename enumtostr.cpp => src/enumtostr.cpp (100%)
rename estring.cpp => src/estring.cpp (100%)
rename estring.h => src/estring.h (100%)
rename fasta.cpp => src/fasta.cpp (100%)
rename fasta2.cpp => src/fasta2.cpp (100%)
rename fastclust.cpp => src/fastclust.cpp (100%)
rename fastdist.cpp => src/fastdist.cpp (100%)
rename fastdistjones.cpp => src/fastdistjones.cpp (100%)
rename fastdistkbit.cpp => src/fastdistkbit.cpp (100%)
rename fastdistkmer.cpp => src/fastdistkmer.cpp (100%)
rename fastdistmafft.cpp => src/fastdistmafft.cpp (100%)
rename fastdistnuc.cpp => src/fastdistnuc.cpp (100%)
rename fastscorepath2.cpp => src/fastscorepath2.cpp (100%)
rename finddiags.cpp => src/finddiags.cpp (100%)
rename finddiagsn.cpp => src/finddiagsn.cpp (100%)
rename gapscoredimer.h => src/gapscoredimer.h (100%)
rename gatest.cpp => src/gatest.cpp (100%)
rename glbalign.cpp => src/glbalign.cpp (100%)
rename glbalign352.cpp => src/glbalign352.cpp (100%)
rename glbaligndiag.cpp => src/glbaligndiag.cpp (100%)
rename glbalignla.cpp => src/glbalignla.cpp (100%)
rename glbalignle.cpp => src/glbalignle.cpp (100%)
rename glbalignns.cpp => src/glbalignns.cpp (100%)
rename glbalignsimple.cpp => src/glbalignsimple.cpp (100%)
rename glbalignsp.cpp => src/glbalignsp.cpp (100%)
rename glbalignspn.cpp => src/glbalignspn.cpp (100%)
rename glbalignss.cpp => src/glbalignss.cpp (100%)
rename glbalndimer.cpp => src/glbalndimer.cpp (100%)
rename globals.cpp => src/globals.cpp (100%)
rename globalslinux.cpp => src/globalslinux.cpp (100%)
rename globalsosx.cpp => src/globalsosx.cpp (100%)
rename globalsother.cpp => src/globalsother.cpp (100%)
rename globalswin32.cpp => src/globalswin32.cpp (100%)
rename gonnet.cpp => src/gonnet.cpp (100%)
rename gonnet.h => src/gonnet.h (100%)
rename gotowt.cpp => src/gotowt.cpp (100%)
rename henikoffweight.cpp => src/henikoffweight.cpp (100%)
rename henikoffweightpb.cpp => src/henikoffweightpb.cpp (100%)
rename html.cpp => src/html.cpp (100%)
rename hydro.cpp => src/hydro.cpp (100%)
rename intmath.cpp => src/intmath.cpp (100%)
rename intmath.h => src/intmath.h (100%)
rename local.cpp => src/local.cpp (100%)
rename main.cpp => src/main.cpp (100%)
rename make.err => src/make.err (100%)
rename make.out => src/make.out (100%)
rename makerootmsa.cpp => src/makerootmsa.cpp (100%)
rename makerootmsab.cpp => src/makerootmsab.cpp (100%)
rename maketree.cpp => src/maketree.cpp (100%)
rename mhack.cpp => src/mhack.cpp (100%)
rename mk => src/mk (100%)
rename mpam200.cpp => src/mpam200.cpp (100%)
rename msa.cpp => src/msa.cpp (100%)
rename msa.h => src/msa.h (100%)
rename msa2.cpp => src/msa2.cpp (100%)
rename msadist.h => src/msadist.h (100%)
rename msadistkimura.cpp => src/msadistkimura.cpp (100%)
rename msadistkimura.h => src/msadistkimura.h (100%)
rename msadistmafft.h => src/msadistmafft.h (100%)
rename msf.cpp => src/msf.cpp (100%)
rename muscle.cpp => src/muscle.cpp (100%)
rename muscle.h => src/muscle.h (100%)
rename muscleout.cpp => src/muscleout.cpp (100%)
rename nucmx.cpp => src/nucmx.cpp (100%)
rename nwdasimple.cpp => src/nwdasimple.cpp (100%)
rename nwdasimple2.cpp => src/nwdasimple2.cpp (100%)
rename nwdasmall.cpp => src/nwdasmall.cpp (100%)
rename nwrec.cpp => src/nwrec.cpp (100%)
rename nwsmall.cpp => src/nwsmall.cpp (100%)
rename objscore.cpp => src/objscore.cpp (100%)
rename objscore.h => src/objscore.h (100%)
rename objscore2.cpp => src/objscore2.cpp (100%)
rename objscoreda.cpp => src/objscoreda.cpp (100%)
rename onexception.cpp => src/onexception.cpp (100%)
rename options.cpp => src/options.cpp (100%)
rename outweights.cpp => src/outweights.cpp (100%)
rename pam200mafft.cpp => src/pam200mafft.cpp (100%)
rename params.cpp => src/params.cpp (100%)
rename params.h => src/params.h (100%)
rename phy.cpp => src/phy.cpp (100%)
rename phy2.cpp => src/phy2.cpp (100%)
rename phy3.cpp => src/phy3.cpp (100%)
rename phy4.cpp => src/phy4.cpp (100%)
rename phyfromclust.cpp => src/phyfromclust.cpp (100%)
rename phyfromfile.cpp => src/phyfromfile.cpp (100%)
rename physeq.cpp => src/physeq.cpp (100%)
rename phytofile.cpp => src/phytofile.cpp (100%)
rename posgap.cpp => src/posgap.cpp (100%)
rename ppscore.cpp => src/ppscore.cpp (100%)
rename profdb.cpp => src/profdb.cpp (100%)
rename profile.cpp => src/profile.cpp (100%)
rename profile.h => src/profile.h (100%)
rename profilefrommsa.cpp => src/profilefrommsa.cpp (100%)
rename progalign.cpp => src/progalign.cpp (100%)
rename progress.cpp => src/progress.cpp (100%)
rename progressivealign.cpp => src/progressivealign.cpp (100%)
rename pwpath.cpp => src/pwpath.cpp (100%)
rename pwpath.h => src/pwpath.h (100%)
rename readmx.cpp => src/readmx.cpp (100%)
rename realigndiffs.cpp => src/realigndiffs.cpp (100%)
rename realigndiffse.cpp => src/realigndiffse.cpp (100%)
rename redblack.cpp => src/redblack.cpp (100%)
rename refine.cpp => src/refine.cpp (100%)
rename refinehoriz.cpp => src/refinehoriz.cpp (100%)
rename refinesubfams.cpp => src/refinesubfams.cpp (100%)
rename refinetree.cpp => src/refinetree.cpp (100%)
rename refinetreee.cpp => src/refinetreee.cpp (100%)
rename refinevert.cpp => src/refinevert.cpp (100%)
rename refinew.cpp => src/refinew.cpp (100%)
rename releases.txt => src/releases.txt (100%)
rename savebest.cpp => src/savebest.cpp (100%)
rename scoredist.cpp => src/scoredist.cpp (100%)
rename scoregaps.cpp => src/scoregaps.cpp (100%)
rename scorehistory.cpp => src/scorehistory.cpp (100%)
rename scorehistory.h => src/scorehistory.h (100%)
rename scoremx.cpp => src/scoremx.cpp (100%)
rename scorepp.cpp => src/scorepp.cpp (100%)
rename seq.cpp => src/seq.cpp (100%)
rename seq.h => src/seq.h (100%)
rename seqvect.cpp => src/seqvect.cpp (100%)
rename seqvect.h => src/seqvect.h (100%)
rename setblosumweights.cpp => src/setblosumweights.cpp (100%)
rename setgscweights.cpp => src/setgscweights.cpp (100%)
rename setnewhandler.cpp => src/setnewhandler.cpp (100%)
rename spfast.cpp => src/spfast.cpp (100%)
rename sptest.cpp => src/sptest.cpp (100%)
rename stabilize.cpp => src/stabilize.cpp (100%)
rename subfam.cpp => src/subfam.cpp (100%)
rename subfams.cpp => src/subfams.cpp (100%)
rename svnmods.h => src/svnmods.h (100%)
rename svnversion.h => src/svnversion.h (100%)
rename sw.cpp => src/sw.cpp (100%)
rename termgaps.cpp => src/termgaps.cpp (100%)
rename textfile.cpp => src/textfile.cpp (100%)
rename textfile.h => src/textfile.h (100%)
rename threewaywt.cpp => src/threewaywt.cpp (100%)
rename timing.h => src/timing.h (100%)
rename tomhydro.cpp => src/tomhydro.cpp (100%)
rename traceback.cpp => src/traceback.cpp (100%)
rename tracebackopt.cpp => src/tracebackopt.cpp (100%)
rename tracebacksw.cpp => src/tracebacksw.cpp (100%)
rename tree.h => src/tree.h (100%)
rename treefrommsa.cpp => src/treefrommsa.cpp (100%)
rename types.h => src/types.h (100%)
rename typetostr.cpp => src/typetostr.cpp (100%)
rename unixio.h => src/unixio.h (100%)
rename upgma2.cpp => src/upgma2.cpp (100%)
rename usage.cpp => src/usage.cpp (100%)
rename validateids.cpp => src/validateids.cpp (100%)
rename version.txt => src/version.txt (100%)
rename vtml2.cpp => src/vtml2.cpp (100%)
rename writescorefile.cpp => src/writescorefile.cpp (100%)
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