[med-svn] [paml] 02/03: Merge tag 'upstream/4.9c+dfsg'
Andreas Tille
tille at debian.org
Thu Oct 6 03:57:24 UTC 2016
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tille pushed a commit to branch master
in repository paml.
commit 4bef5d00ee2030a3ebdf129c4ee8c6379b9af8ba
Merge: 8c7ab84 4fa6da4
Author: Andreas Tille <tille at debian.org>
Date: Thu Oct 6 05:51:59 2016 +0200
Merge tag 'upstream/4.9c+dfsg'
Upstream version 4.9c+dfsg
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(-)
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