paml-4.9e-i586-1_slonly.txz


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Description

paml - PAML: Phylogenetic Analysis by Maximum Likelihood

Property Value
Distribution Slackware 14.2
Repository Slackonly i486
Package name paml
Package version 4.9e
Package release 1_slonly
Package architecture i586
Package type txz
Installed size 12.03 MB
Download size 3.02 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

Alternatives

Package Version Architecture Repository
paml-4.9h-x86_64-1_slonly.txz 4.9h x86_64 Slackonly
paml - - -

Download

Type URL
Binary Package paml-4.9e-i586-1_slonly.txz
Source Package unknown

Install Howto

  1. Download paml-4.9e-i586-1_slonly.txz
  2. Install paml txz package:
    # upgradepkg --install-new paml-4.9e-i586-1_slonly.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-4.9e/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

See Also

Package Description
pamlX-1.3.1-i586-4_slonly.txz A GUI for PAML
pandas-0.20.3-i586-1_slonly.txz Powerful data structures
pandocfilters-1.4.1-i586-1_slonly.txz Python module for writing pandoc filters
pangox-compat-0.0.2-i586-1_slonly.txz X font support for Pango
pangzero-1.4.1+git20121103-noarch-1_slonly.txz clone of arcade game "Super Pang"
paper-gtk-theme-2.1.0-noarch-1_slonly.txz Paper Theme Suite
paper-icon-theme-1.4.0-noarch-1_slonly.txz Paper Icons
paperkey-1.4-i586-1_slonly.txz an OpenPGP key archiver
papi-5.5.1-i586-1_slonly.txz Performance Application Programming Interface
paprefs-0.9.10-i586-1_slonly.txz PulseAudio Preferences
paps-0.6.8-i586-1_slonly.txz Unicode-aware text to PostScript converter
par-1.52-i586-1_slonly.txz paragraph reformatter
par2cmdline-0.7.3-i586-1_slonly.txz Commandline implementation of PARv2.0 specification
par2cmdline-tbb-0.4_20141125-i686-1_slonly.txz a multithreaded version of par2cmdline
parallel-20170622-i586-1_slonly.txz Executes jobs in parallel
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