paml-4.8a-x86_64-3_slack.txz


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Description

paml - PAML: Phylogenetic Analysis by Maximum Likelihood

Property Value
Distribution Slackware 14.1
Repository Slackonly x86_64
Package filename paml-4.8a-x86_64-3_slack.txz
Package name paml
Package version 4.8a
Package release 3_slack
Package architecture x86_64
Package type txz
Homepage -
License -
Maintainer -
Download size 3.04 MB
Installed size 11.99 MB
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-4.8a/References

Alternatives

Package Version Architecture Repository
paml-4.8a-i486-2_slack.txz 4.8a i486 Slackonly
paml - - -

Download

Type URL
Mirror packages.slackonly.com
Binary Package paml-4.8a-x86_64-3_slack.txz
Source Package -

Install Howto

  1. Download paml-4.8a-x86_64-3_slack.txz
  2. Install paml txz package:
    # upgradepkg --install-new paml-4.8a-x86_64-3_slack.txz

Files

Path
/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-4.8a/GeneticCode.txt
/usr/doc/paml-4.8a/LICENSE
/usr/doc/paml-4.8a/MCMCtree.Tutorial.pdf
/usr/doc/paml-4.8a/MCMCtree.Tutorials.pdf
/usr/doc/paml-4.8a/MCMCtreeDOC.pdf
/usr/doc/paml-4.8a/README-codon.txt
/usr/doc/paml-4.8a/README-compiling.txt
/usr/doc/paml-4.8a/README.txt
/usr/doc/paml-4.8a/eigenQREV.pdf
/usr/doc/paml-4.8a/multiruns.txt
/usr/doc/paml-4.8a/paml.SlackBuild
/usr/doc/paml-4.8a/pamlDOC.pdf
/usr/doc/paml-4.8a/pamlFAQs.pdf
/usr/doc/paml-4.8a/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/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/FixedDsClock23.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/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

See Also

Package Description
pamlX-1.3.1-x86_64-2_slack.txz A GUI for PAML
pandas-0.17.1-x86_64-1_slack.txz Powerful data structures
pandoc-1.13.2-x86_64-1_slack.txz markup conversion tool
pangomm-2.34.0-x86_64-1_slack.txz C++ API for Pango
pangox-compat-0.0.2-x86_64-1_slack.txz X font support for Pango
paprefs-0.9.10-x86_64-5_slack.txz PulseAudio Preferences
paps-0.6.8-x86_64-1_slack.txz Unicode-aware text to PostScript converter
par-1.52-x86_64-1_slack.txz paragraph reformatter
par2cmdline-0.6.13-x86_64-1_slack.txz Commandline implementation of PARv2.0 specification
par2cmdline-tbb-0.4_20141125-x86_64-4_slack.txz a multithreaded version of par2cmdline
parallel-20151222-x86_64-1_slack.txz Executes jobs in parallel
paramiko-1.15.2-x86_64-2_slack.txz Python SSH module
paraview-4.0.1-x86_64-1_slack.txz multi-platform data analysis and visualization application
parcellite-1.1.9-x86_64-1_slack.txz clipboard manager
parmetis-4.0.3-x86_64-1_slack.txz parallel library
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