179 lines
9.0 KiB
Plaintext
179 lines
9.0 KiB
Plaintext
bin/baseml
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bin/basemlg
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bin/chi2
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bin/codeml
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bin/evolver
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bin/evolverNSbranches
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bin/evolverNSbranchsites
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bin/evolverNSsites
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bin/infinitesites
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bin/mcmctree
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bin/pamp
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bin/yn00
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%%PORTDOCS%%%%DOCSDIR%%/MCMCtree.Tutorials.pdf
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%%PORTDOCS%%%%DOCSDIR%%/README.md
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%%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf
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%%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf
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%%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3s.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4s.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/5s.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/6s.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/9s.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/ECP_EDN_15.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/PAMLCladeModelCDnotes.pdf
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/codeml.CladeC.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/codeml.CladeD.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/tree.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/BF.Clock23.xlsx
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/BFdriverDOC.pdf
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/FixedDsClock23.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/README.BayesFactor.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/README.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/bf1/mcmctree.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/bf2/mcmctree.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mcmctree.Infinitesites.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mcmctree.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mtCDNApri.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mtCDNApri123.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/GeneticCode.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden4s.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden4s.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/README.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/codeml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCaa.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbase.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbaseRandomTree.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCcodon.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/README.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.phy
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/codeml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs123.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/README.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/README2.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/aaml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/aaml2.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/baseml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/baseml2.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codeml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codonml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codonml2.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/mtmam.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Pt/eigenQREV.pdf
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Pt/testPMat.c
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSbranches.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSbranchsites.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSclade.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSsites.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/PositiveSites.c
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/README.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/codeml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/multiruns.c
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/multiruns.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.Beast.Nulldata.xml
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.Beast.xml
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.NodeNumbers.tre
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.nexus
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.tre
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/baseml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/commands.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/in.BV.HKYG5
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock1.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock2.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock3.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.tre
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/README.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/baseml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/in.BV.HKYG5
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ExactlnL.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/YN00abglobin.result.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/aaml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/baseml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.rooted.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codeml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codonml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dNdSGene1.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/MtZoa.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/cpREV10.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/cpREV64.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/dayhoff-dcmut.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/dayhoff.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974a.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974c.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974p.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974v.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/grantham.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/jones-dcmut.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/jones.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/lg.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/miyata.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtArt.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtREV24.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtmam.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/wag.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/README.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/RasMol.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/SiteNumbering.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/codeml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/codemlYangSwanson2002.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysin.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysin.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysinYangSwanson2002.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/README.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/codeml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mcmctree.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/AAcodon.result.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/README.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/codeml.AAcodon.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/codeml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/miyata.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNAmam.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNAmam.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/2s.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/OmegaAA.dat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/README.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/codeml.HC.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/codeml.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNA.HC.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtprim9.nuc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-mc.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-mc.txt
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupblock
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupend
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupstart
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.trees
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/yn00.ctl
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