Files

• MANIFEST
• META.json
• META.yml
• Makefile.PL
• README
• bin/dssp
• bin/mecom
• docs/mecom.pod
• lib/Mecom.pm
• lib/Mecom/Align/Subset.pm
• lib/Mecom/Bio/Tools/Run/Phylo/PAML/Yn00.pm
• lib/Mecom/Bio/Tools/Run/WrapperBase.pm
• lib/Mecom/Contact.pm
• lib/Mecom/EasyYang.pm
• lib/Mecom/Report.pm
• lib/Mecom/Statistics/RatioVariance.pm
• lib/Mecom/Subsets.pm
• lib/Mecom/Surface.pm
• paml4.7/3s.trees
• paml4.7/4s.trees
• paml4.7/5s.trees
• paml4.7/6s.trees
• paml4.7/GeneticCode.txt
• paml4.7/MCaa.dat
• paml4.7/MCbase.dat
• paml4.7/MCbaseRandomTree.dat
• paml4.7/MCcodon.dat
• paml4.7/README.txt
• paml4.7/Technical/Pt/eigenQREV.pdf
• paml4.7/Technical/Pt/testPMat.c
• paml4.7/Technical/Simulation/Codon/MCcodonNSbranches.dat
• paml4.7/Technical/Simulation/Codon/MCcodonNSbranchsites.dat
• paml4.7/Technical/Simulation/Codon/MCcodonNSsites.dat
• paml4.7/Technical/Simulation/Codon/PositiveSites.c
• paml4.7/Technical/Simulation/Codon/PositiveSitesBEB.exe
• paml4.7/Technical/Simulation/Codon/PositiveSitesBS.exe
• paml4.7/Technical/Simulation/Codon/PositiveSitesNEB.exe
• paml4.7/Technical/Simulation/Codon/README.txt
• paml4.7/Technical/Simulation/Codon/codeml.ctl
• paml4.7/Technical/Simulation/Codon/evolverNSbranches.exe
• paml4.7/Technical/Simulation/Codon/evolverNSbranchsites.exe
• paml4.7/Technical/Simulation/Codon/evolverNSsites.exe
• paml4.7/Technical/Simulation/multiruns.c
• paml4.7/Technical/Simulation/multiruns.exe
• paml4.7/Technical/Simulation/multiruns.txt
• paml4.7/aaml.ctl
• paml4.7/baseml.ctl
• paml4.7/bin/InfiniteSites.exe
• paml4.7/bin/TreeTimeJeff.exe
• paml4.7/bin/baseml.exe
• paml4.7/bin/basemlg.exe
• paml4.7/bin/chi2.exe
• paml4.7/bin/codeml.exe
• paml4.7/bin/ds.exe
• paml4.7/bin/evolver.exe
• paml4.7/bin/mcmctree.exe
• paml4.7/bin/pamp.exe
• paml4.7/bin/yn00.exe
• paml4.7/brown.nuc
• paml4.7/brown.rooted.trees
• paml4.7/brown.trees
• paml4.7/codeml.ctl
• paml4.7/codonml.ctl
• paml4.7/dat/MtZoa.dat
• paml4.7/dat/cpREV10.dat
• paml4.7/dat/cpREV64.dat
• paml4.7/dat/dayhoff-dcmut.dat
• paml4.7/dat/dayhoff.dat
• paml4.7/dat/g1974a.dat
• paml4.7/dat/g1974c.dat
• paml4.7/dat/g1974p.dat
• paml4.7/dat/g1974v.dat
• paml4.7/dat/grantham.dat
• paml4.7/dat/jones-dcmut.dat
• paml4.7/dat/jones.dat
• paml4.7/dat/lg.dat
• paml4.7/dat/miyata.dat
• paml4.7/dat/mtArt.dat
• paml4.7/dat/mtREV24.dat
• paml4.7/dat/mtmam.dat
• paml4.7/dat/wag.dat
• paml4.7/doc/MCMCtree.Tutorial.pdf
• paml4.7/doc/MCMCtreeDOC.pdf
• paml4.7/doc/pamlDOC.pdf
• paml4.7/doc/pamlFAQs.pdf
• paml4.7/doc/pamlHistory.txt
• paml4.7/examples/9s.trees
• paml4.7/examples/CladeModelCD/CladeModelCnotes.doc
• paml4.7/examples/CladeModelCD/CladeModelCnotes.pdf
• paml4.7/examples/CladeModelCD/Dataset1.CladeC/ECP_EDN_15.nuc
• paml4.7/examples/CladeModelCD/Dataset1.CladeC/codeml.ctl
• paml4.7/examples/CladeModelCD/Dataset1.CladeC/rooted.pdf
• paml4.7/examples/CladeModelCD/Dataset1.CladeC/tree.txt
• paml4.7/examples/CladeModelCD/Dataset2.CladeD/ECP_EDN_17.nuc
• paml4.7/examples/CladeModelCD/Dataset2.CladeD/codeml.ctl
• paml4.7/examples/CladeModelCD/Dataset2.CladeD/tree.txt
• paml4.7/examples/CladeModelCD/Dataset2.CladeD/unrooted.pdf
• paml4.7/examples/DatingSoftBound/mcmctree.ctl
• paml4.7/examples/DatingSoftBound/mtCDNApri.trees
• paml4.7/examples/DatingSoftBound/mtCDNApri123.txt
• paml4.7/examples/DatingSoftBound/readme.txt
• paml4.7/examples/HIVNSsites/HIVenvSweden.trees
• paml4.7/examples/HIVNSsites/HIVenvSweden.txt
• paml4.7/examples/HIVNSsites/HIVenvSweden4s.trees
• paml4.7/examples/HIVNSsites/HIVenvSweden4s.txt
• paml4.7/examples/HIVNSsites/README.txt
• paml4.7/examples/HIVNSsites/codeml.ctl
• paml4.7/examples/MHC.Swanson2002MBE/README.txt
• paml4.7/examples/MHC.Swanson2002MBE/bigmhc.phy
• paml4.7/examples/MHC.Swanson2002MBE/bigmhc.trees
• paml4.7/examples/MHC.Swanson2002MBE/codeml.ctl
• paml4.7/examples/MouseLemurs/MouseLemurs.aa
• paml4.7/examples/MouseLemurs/MouseLemurs.nuc
• paml4.7/examples/MouseLemurs/MouseLemurs.trees
• paml4.7/examples/MouseLemurs/MouseLemurs123.nuc
• paml4.7/examples/MouseLemurs/README.txt
• paml4.7/examples/MouseLemurs/README2.txt
• paml4.7/examples/MouseLemurs/aaml.ctl
• paml4.7/examples/MouseLemurs/aaml2.ctl
• paml4.7/examples/MouseLemurs/baseml.ctl
• paml4.7/examples/MouseLemurs/baseml2.ctl
• paml4.7/examples/MouseLemurs/codeml.ctl
• paml4.7/examples/MouseLemurs/codonml.ctl
• paml4.7/examples/MouseLemurs/codonml2.ctl
• paml4.7/examples/MouseLemurs/mtmam.dat
• paml4.7/examples/README.txt
• paml4.7/examples/TipDate.FluH1/H1.Beast.Nulldata.xml
• paml4.7/examples/TipDate.FluH1/H1.Beast.xml
• paml4.7/examples/TipDate.FluH1/H1.NodeNumbers.tre
• paml4.7/examples/TipDate.FluH1/H1.nexus
• paml4.7/examples/TipDate.FluH1/H1.tre
• paml4.7/examples/TipDate.FluH1/H1.txt
• paml4.7/examples/TipDate.FluH1/baseml.ctl
• paml4.7/examples/TipDate.FluH1/commands.txt
• paml4.7/examples/TipDate.FluH1/in.BV.HKYG5
• paml4.7/examples/TipDate.FluH1/mcmctreeClock1.ctl
• paml4.7/examples/TipDate.FluH1/mcmctreeClock2.ctl
• paml4.7/examples/TipDate.FluH1/mcmctreeClock3.ctl
• paml4.7/examples/TipDate.HIV2/HIV2ge.tre
• paml4.7/examples/TipDate.HIV2/HIV2ge.txt
• paml4.7/examples/TipDate.HIV2/README.txt
• paml4.7/examples/TipDate.HIV2/baseml.ctl
• paml4.7/examples/TipDate.HIV2/in.BV.HKYG5
• paml4.7/examples/TipDate.HIV2/mcmctree.ExactlnL.ctl
• paml4.7/examples/TipDate.HIV2/mcmctree.ctl
• paml4.7/examples/YN00abglobin.result
• paml4.7/examples/abglobin.aa
• paml4.7/examples/abglobin.nuc
• paml4.7/examples/abglobin.trees
• paml4.7/examples/dNdSGene1.nuc
• paml4.7/examples/horai.nuc
• paml4.7/examples/horai.trees
• paml4.7/examples/lysin/README.txt
• paml4.7/examples/lysin/RasMol.txt
• paml4.7/examples/lysin/SiteNumbering.txt
• paml4.7/examples/lysin/codeml.ctl
• paml4.7/examples/lysin/codemlYangSwanson2002.ctl
• paml4.7/examples/lysin/lysin.nuc
• paml4.7/examples/lysin/lysin.trees
• paml4.7/examples/lysin/lysinYangSwanson2002.nuc
• paml4.7/examples/lysozyme/README.txt
• paml4.7/examples/lysozyme/codeml.ctl
• paml4.7/examples/lysozyme/lysozymeLarge.ctl
• paml4.7/examples/lysozyme/lysozymeLarge.nuc
• paml4.7/examples/lysozyme/lysozymeLarge.trees
• paml4.7/examples/lysozyme/lysozymeSmall.ctl
• paml4.7/examples/lysozyme/lysozymeSmall.nuc
• paml4.7/examples/lysozyme/lysozymeSmall.trees
• paml4.7/examples/lysozyme/lysozymeSmall.txt
• paml4.7/examples/mtCDNA/README.txt
• paml4.7/examples/mtCDNA/codeml.ctl
• paml4.7/examples/mtCDNA/miyata.dat
• paml4.7/examples/mtCDNA/mtCDNAmam.nuc
• paml4.7/examples/mtCDNA/mtCDNAmam.trees
• paml4.7/examples/mtCDNA/mtCDNApri.aa
• paml4.7/examples/mtCDNA/mtCDNApri.nuc
• paml4.7/examples/mtCDNA/mtCDNApri.trees
• paml4.7/examples/mtCDNAape/2s.trees
• paml4.7/examples/mtCDNAape/OmegaAA.dat
• paml4.7/examples/mtCDNAape/README.txt
• paml4.7/examples/mtCDNAape/codeml.HC.ctl
• paml4.7/examples/mtCDNAape/codeml.ctl
• paml4.7/examples/mtCDNAape/mtCDNA.HC.txt
• paml4.7/examples/mtCDNAape/mtCDNAape.trees
• paml4.7/examples/mtCDNAape/mtCDNAape.txt
• paml4.7/examples/mtprim9.nuc
• paml4.7/mcmctree.ctl
• paml4.7/pamp.ctl
• paml4.7/paupblock
• paml4.7/paupend
• paml4.7/paupstart
• paml4.7/src/Makefile
• paml4.7/src/Makefile.MSVC
• paml4.7/src/README.txt
• paml4.7/src/TreeTimeJeff.c
• paml4.7/src/baseml.c
• paml4.7/src/basemlg.c
• paml4.7/src/chi2.c
• paml4.7/src/codeml.c
• paml4.7/src/ds.c
• paml4.7/src/evolver.c
• paml4.7/src/mcmctree.c
• paml4.7/src/paml.h
• paml4.7/src/pamp.c
• paml4.7/src/tools.c
• paml4.7/src/treespace.c
• paml4.7/src/treesub.c
• paml4.7/src/yn00.c
• paml4.7/stewart.aa
• paml4.7/stewart.trees
• paml4.7/yn00.ctl
• t/00-load.t
• t/manifest.t
• t/pod-coverage.t
• t/pod.t