[med-svn] [paml] branch upstream updated (79cb983 -> 4fa6da4)
Andreas Tille
tille at debian.org
Thu Oct 6 03:57:27 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 79cb983 New upstream version 4.9b+dfsg
new 4fa6da4 New upstream version 4.9c+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
Technical/Simulation/Codon/MCcodonNSclade.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 | 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 | 14 +++
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 | 4 +-
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 | 2 +-
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 | 11 +-
src/TreeTimeJeff.c | 0
src/baseml.c | 0
src/basemlg.c | 0
src/chi2.c | 0
src/codeml.c | 25 ++---
src/ds.c | 0
src/evolver.c | 0
src/mcmctree.c | 0
src/paml.h | 5 +-
src/pamp.c | 0
src/tools.c | 117 ++++++++++++---------
src/treespace.c | 0
src/treesub.c | 111 ++++++++++++-------
src/yn00.c | 0
stewart.aa | 0
stewart.trees | 0
yn00.ctl | 0
167 files changed, 180 insertions(+), 109 deletions(-)
mode change 100755 => 100644 3s.trees
mode change 100755 => 100644 4s.trees
mode change 100755 => 100644 5s.trees
mode change 100755 => 100644 6s.trees
mode change 100755 => 100644 GeneticCode.txt
mode change 100755 => 100644 MCaa.dat
mode change 100755 => 100644 MCbase.dat
mode change 100755 => 100644 MCbaseRandomTree.dat
mode change 100755 => 100644 MCcodon.dat
mode change 100755 => 100644 README.txt
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/MCcodonNSclade.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 aaml.ctl
mode change 100755 => 100644 baseml.ctl
mode change 100755 => 100644 brown.nuc
mode change 100755 => 100644 brown.rooted.trees
mode change 100755 => 100644 brown.trees
mode change 100755 => 100644 codeml.ctl
mode change 100755 => 100644 codonml.ctl
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
mode change 100755 => 100644 examples/9s.trees
mode change 100755 => 100644 examples/CladeModelCD/ECP_EDN_15.nuc
mode change 100755 => 100644 examples/CladeModelCD/codeml.CladeC.ctl
mode change 100755 => 100644 examples/CladeModelCD/codeml.CladeD.ctl
mode change 100755 => 100644 examples/CladeModelCD/tree.txt
mode change 100755 => 100644 examples/DatingSoftBound/FixedDsClock23.txt
mode change 100755 => 100644 examples/DatingSoftBound/README.txt
mode change 100755 => 100644 examples/DatingSoftBound/mcmctree.Infinitesites.ctl
mode change 100755 => 100644 examples/DatingSoftBound/mcmctree.ctl
mode change 100755 => 100644 examples/DatingSoftBound/mtCDNApri.trees
mode change 100755 => 100644 examples/DatingSoftBound/mtCDNApri123.txt
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/README.txt
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
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/YN00abglobin.result
mode change 100755 => 100644 examples/abglobin.aa
mode change 100755 => 100644 examples/abglobin.nuc
mode change 100755 => 100644 examples/abglobin.trees
mode change 100755 => 100644 examples/dNdSGene1.nuc
mode change 100755 => 100644 examples/horai.nuc
mode change 100755 => 100644 examples/horai.trees
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
mode change 100755 => 100644 examples/mtprim9.nuc
mode change 100755 => 100644 mcmctree.ctl
mode change 100755 => 100644 pamp.ctl
mode change 100755 => 100644 paupblock
mode change 100755 => 100644 paupend
mode change 100755 => 100644 paupstart
mode change 100755 => 100644 src/Makefile
mode change 100755 => 100644 src/Makefile.MSVC
mode change 100755 => 100644 src/README.txt
mode change 100755 => 100644 src/TreeTimeJeff.c
mode change 100755 => 100644 src/baseml.c
mode change 100755 => 100644 src/basemlg.c
mode change 100755 => 100644 src/chi2.c
mode change 100755 => 100644 src/codeml.c
mode change 100755 => 100644 src/ds.c
mode change 100755 => 100644 src/evolver.c
mode change 100755 => 100644 src/mcmctree.c
mode change 100755 => 100644 src/paml.h
mode change 100755 => 100644 src/pamp.c
mode change 100755 => 100644 src/tools.c
mode change 100755 => 100644 src/treespace.c
mode change 100755 => 100644 src/treesub.c
mode change 100755 => 100644 src/yn00.c
mode change 100755 => 100644 stewart.aa
mode change 100755 => 100644 stewart.trees
mode change 100755 => 100644 yn00.ctl
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