bin/baseml
bin/basemlg
bin/chi2
bin/codeml
bin/evolver
bin/evolverNSbranches
bin/evolverNSbranchsites
bin/evolverNSsites
bin/infinitesites
bin/mcmctree
bin/pamp
bin/yn00
%%PORTDOCS%%%%DOCSDIR%%/MCMCtree.Tutorials.pdf
%%PORTDOCS%%%%DOCSDIR%%/README.md
%%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf
%%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf
%%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/5s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/6s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/9s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/ECP_EDN_15.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/PAMLCladeModelCDnotes.pdf
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/codeml.CladeC.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/codeml.CladeD.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/tree.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/BF.Clock23.xlsx
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/BFdriverDOC.pdf
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/FixedDsClock23.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/README.BayesFactor.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/bf1/mcmctree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/bf2/mcmctree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mcmctree.Infinitesites.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mcmctree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mtCDNApri.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mtCDNApri123.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/GeneticCode.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden4s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden4s.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCaa.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCaa.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbase.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbase.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbaseRandomTree.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbaseRandomTree.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCcodon.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCcodon.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.phy
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs123.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/README2.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/aaml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/aaml2.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/baseml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/baseml2.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codonml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codonml2.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/mtmam.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Pt/eigenQREV.pdf
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Pt/testPMat.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSbranches.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSbranchsites.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSclade.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSsites.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/PositiveSites.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/multiruns.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/multiruns.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.Beast.Nulldata.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.Beast.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.NodeNumbers.tre
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.nexus
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.tre
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/baseml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/commands.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/in.BV.HKYG5
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock1.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock2.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock3.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.tre
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/baseml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/in.BV.HKYG5
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ExactlnL.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/YN00abglobin.result.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/aaml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/baseml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.rooted.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codonml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dNdSGene1.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/MtZoa.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/cpREV10.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/cpREV64.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/dayhoff-dcmut.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/dayhoff.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974a.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974c.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974p.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974v.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/grantham.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/jones-dcmut.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/jones.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/lg.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/miyata.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtArt.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtREV24.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtmam.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/wag.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/6s-bracing.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/6s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/MCbase-6s.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/mc.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/mcmctree-bracing.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/mcmctree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/RasMol.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/SiteNumbering.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/codemlYangSwanson2002.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysin.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysin.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysinYangSwanson2002.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mcmctree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/AAcodon.result.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/codeml.AAcodon.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/miyata.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNAmam.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNAmam.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/2s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/OmegaAA.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/codeml.HC.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNA.HC.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtprim9.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/codeml-M0.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/myxovirus.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/myxovirus.tree
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata-maintree.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/5s-mc.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/MCbase.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata-maintree-ml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata-maintree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata-maintree-ml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata-maintree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/mc.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/baseml-nhomo4.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/baseml-nhomo5.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/data-MCU0.95-rep1.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo4.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo5.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/rst-nhomo4.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/rst-nhomo5.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/tree-nhomo4.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/tree-nhomo5.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupblock
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupend
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupstart
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/yn00.ctl