paml-4.9e-x86_64-1_slonly.txz


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Description

paml - PAML: Phylogenetic Analysis by Maximum Likelihood

Distribution: Slackware 14.2
Repository: Slackonly x86_64
Package name: paml
Package version: 4.9e
Package release: 1_slonly
Package architecture: x86_64
Package type: txz
Installed size: 12.11 MB
Download size: 3.00 MB
Official Mirror: packages.slackonly.com
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc. Home: http://abacus.gene.ucl.ac.uk/software/paml.html References: /usr/doc/paml-4.9e/References

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    Source package: unknown

    Install Howto

    1. Download paml-4.9e-x86_64-1_slonly.txz
    2. Install paml txz package:
      # upgradepkg --install-new paml-4.9e-x86_64-1_slonly.txz

    Files

    • /install/slack-desc
    • /usr/
    • /usr/bin/baseml
    • /usr/bin/basemlg
    • /usr/bin/chi2
    • /usr/bin/codeml
    • /usr/bin/evolver
    • /usr/bin/mcmctree
    • /usr/bin/pamp
    • /usr/bin/yn00
    • /usr/doc/
    • /usr/doc/paml-4.9e/GeneticCode.txt
    • /usr/doc/paml-4.9e/LICENSE
    • /usr/doc/paml-4.9e/MCMCtree.Tutorial.pdf
    • /usr/doc/paml-4.9e/MCMCtree.Tutorials.pdf
    • /usr/doc/paml-4.9e/MCMCtreeDOC.pdf
    • /usr/doc/paml-4.9e/README-codon.txt
    • /usr/doc/paml-4.9e/README-compiling.txt
    • /usr/doc/paml-4.9e/README.txt
    • /usr/doc/paml-4.9e/eigenQREV.pdf
    • /usr/doc/paml-4.9e/multiruns.txt
    • /usr/doc/paml-4.9e/paml.SlackBuild
    • /usr/doc/paml-4.9e/pamlDOC.pdf
    • /usr/doc/paml-4.9e/pamlFAQs.pdf
    • /usr/doc/paml-4.9e/pamlHistory.txt
    • /usr/doc/paml-4.9e/pamlHistory.txt~
    • /usr/libexec/
    • /usr/libexec/paml/PositiveSitesBEB
    • /usr/libexec/paml/PositiveSitesBS
    • /usr/libexec/paml/PositiveSitesNEB
    • /usr/libexec/paml/TreeTimeJeff
    • /usr/libexec/paml/evolverNSbranches
    • /usr/libexec/paml/evolverNSbranchsites
    • /usr/libexec/paml/evolverNSsites
    • /usr/libexec/paml/multiruns
    • /usr/share/
    • /usr/share/paml/
    • /usr/share/paml/aa/stewart.aa
    • /usr/share/paml/codon/MCcodonNSbranches.dat
    • /usr/share/paml/codon/MCcodonNSbranchsites.dat
    • /usr/share/paml/codon/MCcodonNSclade.dat
    • /usr/share/paml/codon/MCcodonNSsites.dat
    • /usr/share/paml/codon/codeml.ctl
    • /usr/share/paml/ctl/aaml.ctl
    • /usr/share/paml/ctl/baseml.ctl
    • /usr/share/paml/ctl/codeml.ctl
    • /usr/share/paml/ctl/codonml.ctl
    • /usr/share/paml/ctl/mcmctree.ctl
    • /usr/share/paml/ctl/pamp.ctl
    • /usr/share/paml/ctl/yn00.ctl
    • /usr/share/paml/dat/MCaa.dat
    • /usr/share/paml/dat/MCbase.dat
    • /usr/share/paml/dat/MCbaseRandomTree.dat
    • /usr/share/paml/dat/MCcodon.dat
    • /usr/share/paml/dat/MtZoa.dat
    • /usr/share/paml/dat/cpREV10.dat
    • /usr/share/paml/dat/cpREV64.dat
    • /usr/share/paml/dat/dayhoff-dcmut.dat
    • /usr/share/paml/dat/dayhoff.dat
    • /usr/share/paml/dat/g1974a.dat
    • /usr/share/paml/dat/g1974c.dat
    • /usr/share/paml/dat/g1974p.dat
    • /usr/share/paml/dat/g1974v.dat
    • /usr/share/paml/dat/grantham.dat
    • /usr/share/paml/dat/jones-dcmut.dat
    • /usr/share/paml/dat/jones.dat
    • /usr/share/paml/dat/lg.dat
    • /usr/share/paml/dat/miyata.dat
    • /usr/share/paml/dat/mtArt.dat
    • /usr/share/paml/dat/mtREV24.dat
    • /usr/share/paml/dat/mtmam.dat
    • /usr/share/paml/dat/wag.dat
    • /usr/share/paml/examples/9s.trees
    • /usr/share/paml/examples/README.txt
    • /usr/share/paml/examples/YN00abglobin.result
    • /usr/share/paml/examples/abglobin.aa
    • /usr/share/paml/examples/abglobin.nuc
    • /usr/share/paml/examples/abglobin.trees
    • /usr/share/paml/examples/dNdSGene1.nuc
    • /usr/share/paml/examples/horai.nuc
    • /usr/share/paml/examples/horai.trees
    • /usr/share/paml/examples/mtprim9.nuc
    • /usr/share/paml/examples/CladeModelCD/ECP_EDN_15.nuc
    • /usr/share/paml/examples/CladeModelCD/PAMLCladeModelCDnotes.pdf
    • /usr/share/paml/examples/CladeModelCD/codeml.CladeC.ctl
    • /usr/share/paml/examples/CladeModelCD/codeml.CladeD.ctl
    • /usr/share/paml/examples/CladeModelCD/tree.txt
    • /usr/share/paml/examples/DatingSoftBound/BF.Clock23.xlsx
    • /usr/share/paml/examples/DatingSoftBound/BFdriverDOC.pdf
    • /usr/share/paml/examples/DatingSoftBound/FixedDsClock23.txt
    • /usr/share/paml/examples/DatingSoftBound/README.BayesFactor.txt
    • /usr/share/paml/examples/DatingSoftBound/README.txt
    • /usr/share/paml/examples/DatingSoftBound/mcmctree.Infinitesites.ctl
    • /usr/share/paml/examples/DatingSoftBound/mcmctree.ctl
    • /usr/share/paml/examples/DatingSoftBound/mtCDNApri.trees
    • /usr/share/paml/examples/DatingSoftBound/mtCDNApri123.txt
    • /usr/share/paml/examples/DatingSoftBound/bf1/mcmctree.ctl
    • /usr/share/paml/examples/DatingSoftBound/bf2/mcmctree.ctl
    • /usr/share/paml/examples/HIVNSsites/HIVenvSweden.trees
    • /usr/share/paml/examples/HIVNSsites/HIVenvSweden.txt
    • /usr/share/paml/examples/HIVNSsites/HIVenvSweden4s.trees
    • /usr/share/paml/examples/HIVNSsites/HIVenvSweden4s.txt
    • /usr/share/paml/examples/HIVNSsites/README.txt
    • /usr/share/paml/examples/HIVNSsites/codeml.ctl
    • /usr/share/paml/examples/MHC.Swanson2002MBE/README.txt
    • /usr/share/paml/examples/MHC.Swanson2002MBE/bigmhc.phy
    • /usr/share/paml/examples/MHC.Swanson2002MBE/bigmhc.trees
    • /usr/share/paml/examples/MHC.Swanson2002MBE/codeml.ctl
    • /usr/share/paml/examples/MouseLemurs/MouseLemurs.aa
    • /usr/share/paml/examples/MouseLemurs/MouseLemurs.nuc
    • /usr/share/paml/examples/MouseLemurs/MouseLemurs.trees
    • /usr/share/paml/examples/MouseLemurs/MouseLemurs123.nuc
    • /usr/share/paml/examples/MouseLemurs/README.txt
    • /usr/share/paml/examples/MouseLemurs/README2.txt
    • /usr/share/paml/examples/MouseLemurs/aaml.ctl
    • /usr/share/paml/examples/MouseLemurs/aaml2.ctl
    • /usr/share/paml/examples/MouseLemurs/baseml.ctl
    • /usr/share/paml/examples/MouseLemurs/baseml2.ctl
    • /usr/share/paml/examples/MouseLemurs/codeml.ctl
    • /usr/share/paml/examples/MouseLemurs/codonml.ctl
    • /usr/share/paml/examples/MouseLemurs/codonml2.ctl
    • /usr/share/paml/examples/MouseLemurs/mtmam.dat
    • /usr/share/paml/examples/TipDate.FluH1/H1.Beast.Nulldata.xml
    • /usr/share/paml/examples/TipDate.FluH1/H1.Beast.xml
    • /usr/share/paml/examples/TipDate.FluH1/H1.NodeNumbers.tre
    • /usr/share/paml/examples/TipDate.FluH1/H1.nexus
    • /usr/share/paml/examples/TipDate.FluH1/H1.tre
    • /usr/share/paml/examples/TipDate.FluH1/H1.txt
    • /usr/share/paml/examples/TipDate.FluH1/baseml.ctl
    • /usr/share/paml/examples/TipDate.FluH1/commands.txt
    • /usr/share/paml/examples/TipDate.FluH1/in.BV.HKYG5
    • /usr/share/paml/examples/TipDate.FluH1/mcmctreeClock1.ctl
    • /usr/share/paml/examples/TipDate.FluH1/mcmctreeClock2.ctl
    • /usr/share/paml/examples/TipDate.FluH1/mcmctreeClock3.ctl
    • /usr/share/paml/examples/TipDate.HIV2/HIV2ge.tre
    • /usr/share/paml/examples/TipDate.HIV2/HIV2ge.txt
    • /usr/share/paml/examples/TipDate.HIV2/README.txt
    • /usr/share/paml/examples/TipDate.HIV2/baseml.ctl
    • /usr/share/paml/examples/TipDate.HIV2/in.BV.HKYG5
    • /usr/share/paml/examples/TipDate.HIV2/mcmctree.ExactlnL.ctl
    • /usr/share/paml/examples/TipDate.HIV2/mcmctree.ctl
    • /usr/share/paml/examples/lysin/README.txt
    • /usr/share/paml/examples/lysin/RasMol.txt
    • /usr/share/paml/examples/lysin/SiteNumbering.txt
    • /usr/share/paml/examples/lysin/codeml.ctl
    • /usr/share/paml/examples/lysin/codemlYangSwanson2002.ctl
    • /usr/share/paml/examples/lysin/lysin.nuc
    • /usr/share/paml/examples/lysin/lysin.trees
    • /usr/share/paml/examples/lysin/lysinYangSwanson2002.nuc
    • /usr/share/paml/examples/lysozyme/README.txt
    • /usr/share/paml/examples/lysozyme/codeml.ctl
    • /usr/share/paml/examples/lysozyme/lysozymeLarge.ctl
    • /usr/share/paml/examples/lysozyme/lysozymeLarge.nuc
    • /usr/share/paml/examples/lysozyme/lysozymeLarge.trees
    • /usr/share/paml/examples/lysozyme/lysozymeSmall.ctl
    • /usr/share/paml/examples/lysozyme/lysozymeSmall.nuc
    • /usr/share/paml/examples/lysozyme/lysozymeSmall.trees
    • /usr/share/paml/examples/lysozyme/lysozymeSmall.txt
    • /usr/share/paml/examples/mtCDNA/README.txt
    • /usr/share/paml/examples/mtCDNA/codeml.ctl
    • /usr/share/paml/examples/mtCDNA/miyata.dat
    • /usr/share/paml/examples/mtCDNA/mtCDNAmam.nuc
    • /usr/share/paml/examples/mtCDNA/mtCDNAmam.trees
    • /usr/share/paml/examples/mtCDNA/mtCDNApri.aa
    • /usr/share/paml/examples/mtCDNA/mtCDNApri.nuc
    • /usr/share/paml/examples/mtCDNA/mtCDNApri.trees
    • /usr/share/paml/examples/mtCDNAape/2s.trees
    • /usr/share/paml/examples/mtCDNAape/OmegaAA.dat
    • /usr/share/paml/examples/mtCDNAape/README.txt
    • /usr/share/paml/examples/mtCDNAape/codeml.HC.ctl
    • /usr/share/paml/examples/mtCDNAape/codeml.ctl
    • /usr/share/paml/examples/mtCDNAape/mtCDNA.HC.txt
    • /usr/share/paml/examples/mtCDNAape/mtCDNAape.trees
    • /usr/share/paml/examples/mtCDNAape/mtCDNAape.txt
    • /usr/share/paml/nuc/brown.nuc
    • /usr/share/paml/paup/paupblock
    • /usr/share/paml/paup/paupend
    • /usr/share/paml/paup/paupstart
    • /usr/share/paml/trees/3s.trees
    • /usr/share/paml/trees/4s.trees
    • /usr/share/paml/trees/5s.trees
    • /usr/share/paml/trees/6s.trees
    • /usr/share/paml/trees/brown.rooted.trees
    • /usr/share/paml/trees/brown.trees
    • /usr/share/paml/trees/stewart.trees
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