[med-svn] [paml] branch upstream updated (beb5829 -> 79cb983)
Andreas Tille
tille at debian.org
Mon Sep 12 06:48:14 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository paml.
from beb5829 Imported Upstream version 4.91+dfsg
new 79cb983 New upstream version 4.9b+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:
3s.trees | 0
4s.trees | 0
5s.trees | 0
6s.trees | 0
GeneticCode.txt | 0
MCaa.dat | 0
MCbase.dat | 0
MCbaseRandomTree.dat | 0
MCcodon.dat | 0
README.txt | 0
Technical/Pt/testPMat.c | 0
Technical/Simulation/Codon/MCcodonNSbranches.dat | 0
.../Simulation/Codon/MCcodonNSbranchsites.dat | 0
...MCcodonNSbranchsites.dat => MCcodonNSclade.dat} | 11 +-
Technical/Simulation/Codon/MCcodonNSsites.dat | 0
Technical/Simulation/Codon/PositiveSites.c | 0
Technical/Simulation/Codon/README.txt | 0
Technical/Simulation/Codon/codeml.ctl | 0
Technical/Simulation/multiruns.c | 0
Technical/Simulation/multiruns.txt | 0
aaml.ctl | 0
baseml.ctl | 0
brown.nuc | 0
brown.rooted.trees | 0
brown.trees | 0
codeml.ctl | 0
codonml.ctl | 0
dat/MtZoa.dat | 0
dat/cpREV10.dat | 0
dat/cpREV64.dat | 0
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 | 0
dat/wag.dat | 0
doc/pamlHistory.txt | 23 +-
examples/9s.trees | 0
examples/CladeModelCD/ECP_EDN_15.nuc | 0
examples/CladeModelCD/codeml.CladeC.ctl | 0
examples/CladeModelCD/codeml.CladeD.ctl | 0
examples/CladeModelCD/tree.txt | 0
examples/DatingSoftBound/FixedDsClock23.txt | 0
examples/DatingSoftBound/README.txt | 0
.../DatingSoftBound/mcmctree.Infinitesites.ctl | 0
examples/DatingSoftBound/mcmctree.ctl | 0
examples/DatingSoftBound/mtCDNApri.trees | 0
examples/DatingSoftBound/mtCDNApri123.txt | 0
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 | 0
examples/MHC.Swanson2002MBE/codeml.ctl | 0
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/README.txt | 0
examples/TipDate.FluH1/H1.Beast.Nulldata.xml | 0
examples/TipDate.FluH1/H1.Beast.xml | 0
examples/TipDate.FluH1/H1.NodeNumbers.tre | 0
examples/TipDate.FluH1/H1.nexus | 0
examples/TipDate.FluH1/H1.tre | 0
examples/TipDate.FluH1/H1.txt | 0
examples/TipDate.FluH1/baseml.ctl | 0
examples/TipDate.FluH1/commands.txt | 0
examples/TipDate.FluH1/in.BV.HKYG5 | 0
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/YN00abglobin.result | 0
examples/abglobin.aa | 0
examples/abglobin.nuc | 0
examples/abglobin.trees | 0
examples/dNdSGene1.nuc | 0
examples/horai.nuc | 0
examples/horai.trees | 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 | 0
examples/mtCDNAape/codeml.HC.ctl | 0
examples/mtCDNAape/codeml.ctl | 0
examples/mtCDNAape/mtCDNA.HC.txt | 0
examples/mtCDNAape/mtCDNAape.trees | 0
examples/mtCDNAape/mtCDNAape.txt | 0
examples/mtprim9.nuc | 0
mcmctree.ctl | 0
pamp.ctl | 0
paupblock | 0
paupend | 0
paupstart | 0
src/Makefile | 0
src/Makefile.MSVC | 0
src/README.txt | 0
src/TreeTimeJeff.c | 0
src/baseml.c | 1 -
src/basemlg.c | 0
src/chi2.c | 0
src/codeml.c | 769 +++++++++------------
src/ds.c | 0
src/evolver.c | 0
src/mcmctree.c | 17 +-
src/paml.h | 3 +-
src/pamp.c | 0
src/tools.c | 74 +-
src/treespace.c | 0
src/treesub.c | 57 +-
src/yn00.c | 0
stewart.aa | 0
stewart.trees | 0
yn00.ctl | 0
167 files changed, 446 insertions(+), 509 deletions(-)
mode change 100644 => 100755 3s.trees
mode change 100644 => 100755 4s.trees
mode change 100644 => 100755 5s.trees
mode change 100644 => 100755 6s.trees
mode change 100644 => 100755 GeneticCode.txt
mode change 100644 => 100755 MCaa.dat
mode change 100644 => 100755 MCbase.dat
mode change 100644 => 100755 MCbaseRandomTree.dat
mode change 100644 => 100755 MCcodon.dat
mode change 100644 => 100755 README.txt
mode change 100644 => 100755 Technical/Pt/testPMat.c
mode change 100644 => 100755 Technical/Simulation/Codon/MCcodonNSbranches.dat
mode change 100644 => 100755 Technical/Simulation/Codon/MCcodonNSbranchsites.dat
copy Technical/Simulation/Codon/{MCcodonNSbranchsites.dat => MCcodonNSclade.dat} (78%)
mode change 100644 => 100755
mode change 100644 => 100755 Technical/Simulation/Codon/MCcodonNSsites.dat
mode change 100644 => 100755 Technical/Simulation/Codon/PositiveSites.c
mode change 100644 => 100755 Technical/Simulation/Codon/README.txt
mode change 100644 => 100755 Technical/Simulation/Codon/codeml.ctl
mode change 100644 => 100755 Technical/Simulation/multiruns.c
mode change 100644 => 100755 Technical/Simulation/multiruns.txt
mode change 100644 => 100755 aaml.ctl
mode change 100644 => 100755 baseml.ctl
mode change 100644 => 100755 brown.nuc
mode change 100644 => 100755 brown.rooted.trees
mode change 100644 => 100755 brown.trees
mode change 100644 => 100755 codeml.ctl
mode change 100644 => 100755 codonml.ctl
mode change 100644 => 100755 dat/MtZoa.dat
mode change 100644 => 100755 dat/cpREV10.dat
mode change 100644 => 100755 dat/cpREV64.dat
mode change 100644 => 100755 dat/dayhoff-dcmut.dat
mode change 100644 => 100755 dat/dayhoff.dat
mode change 100644 => 100755 dat/g1974a.dat
mode change 100644 => 100755 dat/g1974c.dat
mode change 100644 => 100755 dat/g1974p.dat
mode change 100644 => 100755 dat/g1974v.dat
mode change 100644 => 100755 dat/grantham.dat
mode change 100644 => 100755 dat/jones-dcmut.dat
mode change 100644 => 100755 dat/jones.dat
mode change 100644 => 100755 dat/lg.dat
mode change 100644 => 100755 dat/miyata.dat
mode change 100644 => 100755 dat/mtArt.dat
mode change 100644 => 100755 dat/mtREV24.dat
mode change 100644 => 100755 dat/mtmam.dat
mode change 100644 => 100755 dat/wag.dat
mode change 100644 => 100755 examples/9s.trees
mode change 100644 => 100755 examples/CladeModelCD/ECP_EDN_15.nuc
mode change 100644 => 100755 examples/CladeModelCD/codeml.CladeC.ctl
mode change 100644 => 100755 examples/CladeModelCD/codeml.CladeD.ctl
mode change 100644 => 100755 examples/CladeModelCD/tree.txt
mode change 100644 => 100755 examples/DatingSoftBound/FixedDsClock23.txt
mode change 100644 => 100755 examples/DatingSoftBound/README.txt
mode change 100644 => 100755 examples/DatingSoftBound/mcmctree.Infinitesites.ctl
mode change 100644 => 100755 examples/DatingSoftBound/mcmctree.ctl
mode change 100644 => 100755 examples/DatingSoftBound/mtCDNApri.trees
mode change 100644 => 100755 examples/DatingSoftBound/mtCDNApri123.txt
mode change 100644 => 100755 examples/HIVNSsites/HIVenvSweden.trees
mode change 100644 => 100755 examples/HIVNSsites/HIVenvSweden.txt
mode change 100644 => 100755 examples/HIVNSsites/HIVenvSweden4s.trees
mode change 100644 => 100755 examples/HIVNSsites/HIVenvSweden4s.txt
mode change 100644 => 100755 examples/HIVNSsites/README.txt
mode change 100644 => 100755 examples/HIVNSsites/codeml.ctl
mode change 100644 => 100755 examples/MHC.Swanson2002MBE/README.txt
mode change 100644 => 100755 examples/MHC.Swanson2002MBE/bigmhc.phy
mode change 100644 => 100755 examples/MHC.Swanson2002MBE/bigmhc.trees
mode change 100644 => 100755 examples/MHC.Swanson2002MBE/codeml.ctl
mode change 100644 => 100755 examples/MouseLemurs/MouseLemurs.aa
mode change 100644 => 100755 examples/MouseLemurs/MouseLemurs.nuc
mode change 100644 => 100755 examples/MouseLemurs/MouseLemurs.trees
mode change 100644 => 100755 examples/MouseLemurs/MouseLemurs123.nuc
mode change 100644 => 100755 examples/MouseLemurs/README.txt
mode change 100644 => 100755 examples/MouseLemurs/README2.txt
mode change 100644 => 100755 examples/MouseLemurs/aaml.ctl
mode change 100644 => 100755 examples/MouseLemurs/aaml2.ctl
mode change 100644 => 100755 examples/MouseLemurs/baseml.ctl
mode change 100644 => 100755 examples/MouseLemurs/baseml2.ctl
mode change 100644 => 100755 examples/MouseLemurs/codeml.ctl
mode change 100644 => 100755 examples/MouseLemurs/codonml.ctl
mode change 100644 => 100755 examples/MouseLemurs/codonml2.ctl
mode change 100644 => 100755 examples/MouseLemurs/mtmam.dat
mode change 100644 => 100755 examples/README.txt
mode change 100644 => 100755 examples/TipDate.FluH1/H1.Beast.Nulldata.xml
mode change 100644 => 100755 examples/TipDate.FluH1/H1.Beast.xml
mode change 100644 => 100755 examples/TipDate.FluH1/H1.NodeNumbers.tre
mode change 100644 => 100755 examples/TipDate.FluH1/H1.nexus
mode change 100644 => 100755 examples/TipDate.FluH1/H1.tre
mode change 100644 => 100755 examples/TipDate.FluH1/H1.txt
mode change 100644 => 100755 examples/TipDate.FluH1/baseml.ctl
mode change 100644 => 100755 examples/TipDate.FluH1/commands.txt
mode change 100644 => 100755 examples/TipDate.FluH1/in.BV.HKYG5
mode change 100644 => 100755 examples/TipDate.FluH1/mcmctreeClock1.ctl
mode change 100644 => 100755 examples/TipDate.FluH1/mcmctreeClock2.ctl
mode change 100644 => 100755 examples/TipDate.FluH1/mcmctreeClock3.ctl
mode change 100644 => 100755 examples/TipDate.HIV2/HIV2ge.tre
mode change 100644 => 100755 examples/TipDate.HIV2/HIV2ge.txt
mode change 100644 => 100755 examples/TipDate.HIV2/README.txt
mode change 100644 => 100755 examples/TipDate.HIV2/baseml.ctl
mode change 100644 => 100755 examples/TipDate.HIV2/in.BV.HKYG5
mode change 100644 => 100755 examples/TipDate.HIV2/mcmctree.ExactlnL.ctl
mode change 100644 => 100755 examples/TipDate.HIV2/mcmctree.ctl
mode change 100644 => 100755 examples/YN00abglobin.result
mode change 100644 => 100755 examples/abglobin.aa
mode change 100644 => 100755 examples/abglobin.nuc
mode change 100644 => 100755 examples/abglobin.trees
mode change 100644 => 100755 examples/dNdSGene1.nuc
mode change 100644 => 100755 examples/horai.nuc
mode change 100644 => 100755 examples/horai.trees
mode change 100644 => 100755 examples/lysin/README.txt
mode change 100644 => 100755 examples/lysin/RasMol.txt
mode change 100644 => 100755 examples/lysin/SiteNumbering.txt
mode change 100644 => 100755 examples/lysin/codeml.ctl
mode change 100644 => 100755 examples/lysin/codemlYangSwanson2002.ctl
mode change 100644 => 100755 examples/lysin/lysin.nuc
mode change 100644 => 100755 examples/lysin/lysin.trees
mode change 100644 => 100755 examples/lysin/lysinYangSwanson2002.nuc
mode change 100644 => 100755 examples/lysozyme/README.txt
mode change 100644 => 100755 examples/lysozyme/codeml.ctl
mode change 100644 => 100755 examples/lysozyme/lysozymeLarge.ctl
mode change 100644 => 100755 examples/lysozyme/lysozymeLarge.nuc
mode change 100644 => 100755 examples/lysozyme/lysozymeLarge.trees
mode change 100644 => 100755 examples/lysozyme/lysozymeSmall.ctl
mode change 100644 => 100755 examples/lysozyme/lysozymeSmall.nuc
mode change 100644 => 100755 examples/lysozyme/lysozymeSmall.trees
mode change 100644 => 100755 examples/lysozyme/lysozymeSmall.txt
mode change 100644 => 100755 examples/mtCDNA/README.txt
mode change 100644 => 100755 examples/mtCDNA/codeml.ctl
mode change 100644 => 100755 examples/mtCDNA/miyata.dat
mode change 100644 => 100755 examples/mtCDNA/mtCDNAmam.nuc
mode change 100644 => 100755 examples/mtCDNA/mtCDNAmam.trees
mode change 100644 => 100755 examples/mtCDNA/mtCDNApri.aa
mode change 100644 => 100755 examples/mtCDNA/mtCDNApri.nuc
mode change 100644 => 100755 examples/mtCDNA/mtCDNApri.trees
mode change 100644 => 100755 examples/mtCDNAape/2s.trees
mode change 100644 => 100755 examples/mtCDNAape/OmegaAA.dat
mode change 100644 => 100755 examples/mtCDNAape/README.txt
mode change 100644 => 100755 examples/mtCDNAape/codeml.HC.ctl
mode change 100644 => 100755 examples/mtCDNAape/codeml.ctl
mode change 100644 => 100755 examples/mtCDNAape/mtCDNA.HC.txt
mode change 100644 => 100755 examples/mtCDNAape/mtCDNAape.trees
mode change 100644 => 100755 examples/mtCDNAape/mtCDNAape.txt
mode change 100644 => 100755 examples/mtprim9.nuc
mode change 100644 => 100755 mcmctree.ctl
mode change 100644 => 100755 pamp.ctl
mode change 100644 => 100755 paupblock
mode change 100644 => 100755 paupend
mode change 100644 => 100755 paupstart
mode change 100644 => 100755 src/Makefile
mode change 100644 => 100755 src/Makefile.MSVC
mode change 100644 => 100755 src/README.txt
mode change 100644 => 100755 src/TreeTimeJeff.c
mode change 100644 => 100755 src/baseml.c
mode change 100644 => 100755 src/basemlg.c
mode change 100644 => 100755 src/chi2.c
mode change 100644 => 100755 src/codeml.c
mode change 100644 => 100755 src/ds.c
mode change 100644 => 100755 src/evolver.c
mode change 100644 => 100755 src/mcmctree.c
mode change 100644 => 100755 src/paml.h
mode change 100644 => 100755 src/pamp.c
mode change 100644 => 100755 src/tools.c
mode change 100644 => 100755 src/treespace.c
mode change 100644 => 100755 src/treesub.c
mode change 100644 => 100755 src/yn00.c
mode change 100644 => 100755 stewart.aa
mode change 100644 => 100755 stewart.trees
mode change 100644 => 100755 yn00.ctl
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