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import paml4.8 master paml/4.8a
authorDon Armstrong <don@donarmstrong.com>
Thu, 21 Jan 2016 17:24:10 +0000 (11:24 -0600)
committerDon Armstrong <don@donarmstrong.com>
Thu, 21 Jan 2016 17:24:10 +0000 (11:24 -0600)
commit0dd1f3e913b44bcebd09bd75b0ec79851b55327a
tree945b4ac5fdc227313013768a180b5137fefd8bc7tree | snapshot
import paml4.8
173 files changed:
.gitignore [new file with mode: 0644] blob
3s.trees [new file with mode: 0644] blob
4s.trees [new file with mode: 0644] blob
5s.trees [new file with mode: 0644] blob
6s.trees [new file with mode: 0644] blob
GeneticCode.txt [new file with mode: 0644] blob
MCaa.dat [new file with mode: 0644] blob
MCbase.dat [new file with mode: 0644] blob
MCbaseRandomTree.dat [new file with mode: 0644] blob
MCcodon.dat [new file with mode: 0644] blob
README.txt [new file with mode: 0644] blob
Technical/Pt/eigenQREV.pdf [new file with mode: 0644] blob
Technical/Pt/testPMat.c [new file with mode: 0644] blob
Technical/Simulation/Codon/MCcodonNSbranches.dat [new file with mode: 0644] blob
Technical/Simulation/Codon/MCcodonNSbranchsites.dat [new file with mode: 0644] blob
Technical/Simulation/Codon/MCcodonNSsites.dat [new file with mode: 0644] blob
Technical/Simulation/Codon/PositiveSites.c [new file with mode: 0644] blob
Technical/Simulation/Codon/README.txt [new file with mode: 0644] blob
Technical/Simulation/Codon/codeml.ctl [new file with mode: 0644] blob
Technical/Simulation/multiruns.c [new file with mode: 0644] blob
Technical/Simulation/multiruns.txt [new file with mode: 0644] blob
aaml.ctl [new file with mode: 0644] blob
baseml.ctl [new file with mode: 0644] blob
brown.nuc [new file with mode: 0644] blob
brown.rooted.trees [new file with mode: 0644] blob
brown.trees [new file with mode: 0644] blob
codeml.ctl [new file with mode: 0644] blob
codonml.ctl [new file with mode: 0644] blob
dat/MtZoa.dat [new file with mode: 0644] blob
dat/cpREV10.dat [new file with mode: 0644] blob
dat/cpREV64.dat [new file with mode: 0644] blob
dat/dayhoff-dcmut.dat [new file with mode: 0644] blob
dat/dayhoff.dat [new file with mode: 0644] blob
dat/g1974a.dat [new file with mode: 0644] blob
dat/g1974c.dat [new file with mode: 0644] blob
dat/g1974p.dat [new file with mode: 0644] blob
dat/g1974v.dat [new file with mode: 0644] blob
dat/grantham.dat [new file with mode: 0644] blob
dat/jones-dcmut.dat [new file with mode: 0644] blob
dat/jones.dat [new file with mode: 0644] blob
dat/lg.dat [new file with mode: 0644] blob
dat/miyata.dat [new file with mode: 0644] blob
dat/mtArt.dat [new file with mode: 0644] blob
dat/mtREV24.dat [new file with mode: 0644] blob
dat/mtmam.dat [new file with mode: 0644] blob
dat/wag.dat [new file with mode: 0644] blob
doc/MCMCtree.Tutorials.pdf [new file with mode: 0644] blob
doc/MCMCtreeDOC.pdf [new file with mode: 0644] blob
doc/pamlDOC.pdf [new file with mode: 0644] blob
doc/pamlFAQs.pdf [new file with mode: 0644] blob
doc/pamlHistory.txt [new file with mode: 0644] blob
examples/9s.trees [new file with mode: 0644] blob
examples/CladeModelCD/ECP_EDN_15.nuc [new file with mode: 0644] blob
examples/CladeModelCD/PAMLCladeModelCDnotes.pdf [new file with mode: 0644] blob
examples/CladeModelCD/codeml.CladeC.ctl [new file with mode: 0644] blob
examples/CladeModelCD/codeml.CladeD.ctl [new file with mode: 0644] blob
examples/CladeModelCD/tree.txt [new file with mode: 0644] blob
examples/DatingSoftBound/FixedDsClock23.txt [new file with mode: 0644] blob
examples/DatingSoftBound/README.txt [new file with mode: 0644] blob
examples/DatingSoftBound/mcmctree.Infinitesites.ctl [new file with mode: 0644] blob
examples/DatingSoftBound/mcmctree.ctl [new file with mode: 0644] blob
examples/DatingSoftBound/mtCDNApri.trees [new file with mode: 0644] blob
examples/DatingSoftBound/mtCDNApri123.txt [new file with mode: 0644] blob
examples/HIVNSsites/HIVenvSweden.trees [new file with mode: 0644] blob
examples/HIVNSsites/HIVenvSweden.txt [new file with mode: 0644] blob
examples/HIVNSsites/HIVenvSweden4s.trees [new file with mode: 0644] blob
examples/HIVNSsites/HIVenvSweden4s.txt [new file with mode: 0644] blob
examples/HIVNSsites/README.txt [new file with mode: 0644] blob
examples/HIVNSsites/codeml.ctl [new file with mode: 0644] blob
examples/MHC.Swanson2002MBE/README.txt [new file with mode: 0644] blob
examples/MHC.Swanson2002MBE/bigmhc.phy [new file with mode: 0644] blob
examples/MHC.Swanson2002MBE/bigmhc.trees [new file with mode: 0644] blob
examples/MHC.Swanson2002MBE/codeml.ctl [new file with mode: 0644] blob
examples/MouseLemurs/MouseLemurs.aa [new file with mode: 0644] blob
examples/MouseLemurs/MouseLemurs.nuc [new file with mode: 0644] blob
examples/MouseLemurs/MouseLemurs.trees [new file with mode: 0644] blob
examples/MouseLemurs/MouseLemurs123.nuc [new file with mode: 0644] blob
examples/MouseLemurs/README.txt [new file with mode: 0644] blob
examples/MouseLemurs/README2.txt [new file with mode: 0644] blob
examples/MouseLemurs/aaml.ctl [new file with mode: 0644] blob
examples/MouseLemurs/aaml2.ctl [new file with mode: 0644] blob
examples/MouseLemurs/baseml.ctl [new file with mode: 0644] blob
examples/MouseLemurs/baseml2.ctl [new file with mode: 0644] blob
examples/MouseLemurs/codeml.ctl [new file with mode: 0644] blob
examples/MouseLemurs/codonml.ctl [new file with mode: 0644] blob
examples/MouseLemurs/codonml2.ctl [new file with mode: 0644] blob
examples/MouseLemurs/mtmam.dat [new file with mode: 0644] blob
examples/README.txt [new file with mode: 0644] blob
examples/TipDate.FluH1/H1.Beast.Nulldata.xml [new file with mode: 0644] blob
examples/TipDate.FluH1/H1.Beast.xml [new file with mode: 0644] blob
examples/TipDate.FluH1/H1.NodeNumbers.tre [new file with mode: 0644] blob
examples/TipDate.FluH1/H1.nexus [new file with mode: 0644] blob
examples/TipDate.FluH1/H1.tre [new file with mode: 0644] blob
examples/TipDate.FluH1/H1.txt [new file with mode: 0644] blob
examples/TipDate.FluH1/baseml.ctl [new file with mode: 0644] blob
examples/TipDate.FluH1/commands.txt [new file with mode: 0644] blob
examples/TipDate.FluH1/in.BV.HKYG5 [new file with mode: 0644] blob
examples/TipDate.FluH1/mcmctreeClock1.ctl [new file with mode: 0644] blob
examples/TipDate.FluH1/mcmctreeClock2.ctl [new file with mode: 0644] blob
examples/TipDate.FluH1/mcmctreeClock3.ctl [new file with mode: 0644] blob
examples/TipDate.HIV2/HIV2ge.tre [new file with mode: 0644] blob
examples/TipDate.HIV2/HIV2ge.txt [new file with mode: 0644] blob
examples/TipDate.HIV2/README.txt [new file with mode: 0644] blob
examples/TipDate.HIV2/baseml.ctl [new file with mode: 0644] blob
examples/TipDate.HIV2/in.BV.HKYG5 [new file with mode: 0644] blob
examples/TipDate.HIV2/mcmctree.ExactlnL.ctl [new file with mode: 0644] blob
examples/TipDate.HIV2/mcmctree.ctl [new file with mode: 0644] blob
examples/YN00abglobin.result [new file with mode: 0644] blob
examples/abglobin.aa [new file with mode: 0644] blob
examples/abglobin.nuc [new file with mode: 0644] blob
examples/abglobin.trees [new file with mode: 0644] blob
examples/dNdSGene1.nuc [new file with mode: 0644] blob
examples/horai.nuc [new file with mode: 0644] blob
examples/horai.trees [new file with mode: 0644] blob
examples/lysin/README.txt [new file with mode: 0644] blob
examples/lysin/RasMol.txt [new file with mode: 0644] blob
examples/lysin/SiteNumbering.txt [new file with mode: 0644] blob
examples/lysin/codeml.ctl [new file with mode: 0644] blob
examples/lysin/codemlYangSwanson2002.ctl [new file with mode: 0644] blob
examples/lysin/lysin.nuc [new file with mode: 0644] blob
examples/lysin/lysin.trees [new file with mode: 0644] blob
examples/lysin/lysinYangSwanson2002.nuc [new file with mode: 0644] blob
examples/lysozyme/README.txt [new file with mode: 0644] blob
examples/lysozyme/codeml.ctl [new file with mode: 0644] blob
examples/lysozyme/lysozymeLarge.ctl [new file with mode: 0644] blob
examples/lysozyme/lysozymeLarge.nuc [new file with mode: 0644] blob
examples/lysozyme/lysozymeLarge.trees [new file with mode: 0644] blob
examples/lysozyme/lysozymeSmall.ctl [new file with mode: 0644] blob
examples/lysozyme/lysozymeSmall.nuc [new file with mode: 0644] blob
examples/lysozyme/lysozymeSmall.trees [new file with mode: 0644] blob
examples/lysozyme/lysozymeSmall.txt [new file with mode: 0644] blob
examples/mtCDNA/README.txt [new file with mode: 0644] blob
examples/mtCDNA/codeml.ctl [new file with mode: 0644] blob
examples/mtCDNA/miyata.dat [new file with mode: 0644] blob
examples/mtCDNA/mtCDNAmam.nuc [new file with mode: 0644] blob
examples/mtCDNA/mtCDNAmam.trees [new file with mode: 0644] blob
examples/mtCDNA/mtCDNApri.aa [new file with mode: 0644] blob
examples/mtCDNA/mtCDNApri.nuc [new file with mode: 0644] blob
examples/mtCDNA/mtCDNApri.trees [new file with mode: 0644] blob
examples/mtCDNAape/2s.trees [new file with mode: 0644] blob
examples/mtCDNAape/OmegaAA.dat [new file with mode: 0644] blob
examples/mtCDNAape/README.txt [new file with mode: 0644] blob
examples/mtCDNAape/codeml.HC.ctl [new file with mode: 0644] blob
examples/mtCDNAape/codeml.ctl [new file with mode: 0644] blob
examples/mtCDNAape/mtCDNA.HC.txt [new file with mode: 0644] blob
examples/mtCDNAape/mtCDNAape.trees [new file with mode: 0644] blob
examples/mtCDNAape/mtCDNAape.txt [new file with mode: 0644] blob
examples/mtprim9.nuc [new file with mode: 0644] blob
mcmctree.ctl [new file with mode: 0644] blob
pamp.ctl [new file with mode: 0644] blob
paupblock [new file with mode: 0644] blob
paupend [new file with mode: 0644] blob
paupstart [new file with mode: 0644] blob
src/Makefile [new file with mode: 0644] blob
src/Makefile.MSVC [new file with mode: 0644] blob
src/README.txt [new file with mode: 0644] blob
src/TreeTimeJeff.c [new file with mode: 0644] blob
src/baseml.c [new file with mode: 0644] blob
src/basemlg.c [new file with mode: 0644] blob
src/chi2.c [new file with mode: 0644] blob
src/codeml.c [new file with mode: 0644] blob
src/ds.c [new file with mode: 0644] blob
src/evolver.c [new file with mode: 0644] blob
src/mcmctree.c [new file with mode: 0644] blob
src/paml.h [new file with mode: 0644] blob
src/pamp.c [new file with mode: 0644] blob
src/tools.c [new file with mode: 0644] blob
src/treespace.c [new file with mode: 0644] blob
src/treesub.c [new file with mode: 0644] blob
src/yn00.c [new file with mode: 0644] blob
stewart.aa [new file with mode: 0644] blob
stewart.trees [new file with mode: 0644] blob
yn00.ctl [new file with mode: 0644] blob
Unnamed repository; edit this file 'description' to name the repository.