paml-doc_4.9h+dfsg-1_all.deb


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Description

paml-doc - Documentation for PAML

Property Value
Distribution Ubuntu 19.04 (Disco Dingo)
Repository Ubuntu Universe amd64
Package filename paml-doc_4.9h+dfsg-1_all.deb
Package name paml-doc
Package version 4.9h+dfsg
Package release 1
Package architecture all
Package type deb
Category universe/doc
Homepage http://abacus.gene.ucl.ac.uk/software/paml.html
License -
Maintainer Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Download size 1.24 MB
Installed size 1.38 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.
The source code comes with a series of PDF files to help with
further insights for the working of, and with, PAML.

Alternatives

Package Version Architecture Repository
paml-doc_4.9h+dfsg-1_all.deb 4.9h+dfsg all Ubuntu Universe
paml-doc - - -

Download

Type URL
Mirror archive.ubuntu.com
Binary Package paml-doc_4.9h+dfsg-1_all.deb
Source Package paml

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install paml-doc deb package:
    # sudo apt-get install paml-doc

Files

Path
/usr/share/doc/paml/pamlHistory.txt.gz
/usr/share/doc/paml-doc/README.Debian
/usr/share/doc/paml-doc/changelog.Debian.gz
/usr/share/doc/paml-doc/copyright
/usr/share/doc/paml/examples/9s.trees
/usr/share/doc/paml/examples/README.txt
/usr/share/doc/paml/examples/YN00abglobin.result
/usr/share/doc/paml/examples/abglobin.aa
/usr/share/doc/paml/examples/abglobin.nuc.gz
/usr/share/doc/paml/examples/abglobin.trees
/usr/share/doc/paml/examples/dNdSGene1.nuc.gz
/usr/share/doc/paml/examples/horai.nuc.gz
/usr/share/doc/paml/examples/horai.trees
/usr/share/doc/paml/examples/mtprim9.nuc.gz
/usr/share/doc/paml/examples/CladeModelCD/ECP_EDN_15.nuc.gz
/usr/share/doc/paml/examples/CladeModelCD/codeml.CladeC.ctl
/usr/share/doc/paml/examples/CladeModelCD/codeml.CladeD.ctl
/usr/share/doc/paml/examples/CladeModelCD/tree.txt
/usr/share/doc/paml/examples/DatingSoftBound/BF.Clock23.xlsx.gz
/usr/share/doc/paml/examples/DatingSoftBound/FixedDsClock23.txt
/usr/share/doc/paml/examples/DatingSoftBound/README.BayesFactor.txt
/usr/share/doc/paml/examples/DatingSoftBound/README.txt
/usr/share/doc/paml/examples/DatingSoftBound/mcmctree.Infinitesites.ctl
/usr/share/doc/paml/examples/DatingSoftBound/mcmctree.ctl
/usr/share/doc/paml/examples/DatingSoftBound/mtCDNApri.trees
/usr/share/doc/paml/examples/DatingSoftBound/mtCDNApri123.txt.gz
/usr/share/doc/paml/examples/DatingSoftBound/bf1/mcmctree.ctl
/usr/share/doc/paml/examples/DatingSoftBound/bf2/mcmctree.ctl
/usr/share/doc/paml/examples/HIVNSsites/HIVenvSweden.trees
/usr/share/doc/paml/examples/HIVNSsites/HIVenvSweden.txt
/usr/share/doc/paml/examples/HIVNSsites/HIVenvSweden4s.trees
/usr/share/doc/paml/examples/HIVNSsites/HIVenvSweden4s.txt
/usr/share/doc/paml/examples/HIVNSsites/README.txt
/usr/share/doc/paml/examples/HIVNSsites/codeml.ctl
/usr/share/doc/paml/examples/MHC.Swanson2002MBE/README.txt
/usr/share/doc/paml/examples/MHC.Swanson2002MBE/bigmhc.phy.gz
/usr/share/doc/paml/examples/MHC.Swanson2002MBE/bigmhc.trees.gz
/usr/share/doc/paml/examples/MHC.Swanson2002MBE/codeml.ctl
/usr/share/doc/paml/examples/MouseLemurs/MouseLemurs.aa.gz
/usr/share/doc/paml/examples/MouseLemurs/MouseLemurs.nuc.gz
/usr/share/doc/paml/examples/MouseLemurs/MouseLemurs.trees
/usr/share/doc/paml/examples/MouseLemurs/MouseLemurs123.nuc.gz
/usr/share/doc/paml/examples/MouseLemurs/README.txt.gz
/usr/share/doc/paml/examples/MouseLemurs/README2.txt.gz
/usr/share/doc/paml/examples/MouseLemurs/aaml.ctl
/usr/share/doc/paml/examples/MouseLemurs/aaml2.ctl
/usr/share/doc/paml/examples/MouseLemurs/baseml.ctl
/usr/share/doc/paml/examples/MouseLemurs/baseml2.ctl
/usr/share/doc/paml/examples/MouseLemurs/codeml.ctl
/usr/share/doc/paml/examples/MouseLemurs/codonml.ctl
/usr/share/doc/paml/examples/MouseLemurs/codonml2.ctl
/usr/share/doc/paml/examples/MouseLemurs/mtmam.dat
/usr/share/doc/paml/examples/TipDate.FluH1/H1.Beast.Nulldata.xml.gz
/usr/share/doc/paml/examples/TipDate.FluH1/H1.Beast.xml.gz
/usr/share/doc/paml/examples/TipDate.FluH1/H1.NodeNumbers.tre.gz
/usr/share/doc/paml/examples/TipDate.FluH1/H1.nexus.gz
/usr/share/doc/paml/examples/TipDate.FluH1/H1.tre.gz
/usr/share/doc/paml/examples/TipDate.FluH1/H1.txt.gz
/usr/share/doc/paml/examples/TipDate.FluH1/baseml.ctl
/usr/share/doc/paml/examples/TipDate.FluH1/commands.txt
/usr/share/doc/paml/examples/TipDate.FluH1/in.BV.HKYG5.gz
/usr/share/doc/paml/examples/TipDate.FluH1/mcmctreeClock1.ctl
/usr/share/doc/paml/examples/TipDate.FluH1/mcmctreeClock2.ctl
/usr/share/doc/paml/examples/TipDate.FluH1/mcmctreeClock3.ctl
/usr/share/doc/paml/examples/TipDate.HIV2/HIV2ge.tre
/usr/share/doc/paml/examples/TipDate.HIV2/HIV2ge.txt.gz
/usr/share/doc/paml/examples/TipDate.HIV2/README.txt
/usr/share/doc/paml/examples/TipDate.HIV2/baseml.ctl
/usr/share/doc/paml/examples/TipDate.HIV2/in.BV.HKYG5.gz
/usr/share/doc/paml/examples/TipDate.HIV2/mcmctree.ExactlnL.ctl
/usr/share/doc/paml/examples/TipDate.HIV2/mcmctree.ctl
/usr/share/doc/paml/examples/lysin/README.txt.gz
/usr/share/doc/paml/examples/lysin/RasMol.txt.gz
/usr/share/doc/paml/examples/lysin/SiteNumbering.txt
/usr/share/doc/paml/examples/lysin/codeml.ctl
/usr/share/doc/paml/examples/lysin/codemlYangSwanson2002.ctl
/usr/share/doc/paml/examples/lysin/lysin.nuc.gz
/usr/share/doc/paml/examples/lysin/lysin.trees
/usr/share/doc/paml/examples/lysin/lysinYangSwanson2002.nuc.gz
/usr/share/doc/paml/examples/lysozyme/README.txt.gz
/usr/share/doc/paml/examples/lysozyme/codeml.ctl
/usr/share/doc/paml/examples/lysozyme/lysozymeLarge.ctl
/usr/share/doc/paml/examples/lysozyme/lysozymeLarge.nuc.gz
/usr/share/doc/paml/examples/lysozyme/lysozymeLarge.trees
/usr/share/doc/paml/examples/lysozyme/lysozymeSmall.ctl
/usr/share/doc/paml/examples/lysozyme/lysozymeSmall.nuc.gz
/usr/share/doc/paml/examples/lysozyme/lysozymeSmall.trees
/usr/share/doc/paml/examples/lysozyme/lysozymeSmall.txt
/usr/share/doc/paml/examples/mtCDNA/AAcodon.result.txt.gz
/usr/share/doc/paml/examples/mtCDNA/README.txt
/usr/share/doc/paml/examples/mtCDNA/codeml.AAcodon.ctl
/usr/share/doc/paml/examples/mtCDNA/codeml.ctl
/usr/share/doc/paml/examples/mtCDNA/miyata.dat
/usr/share/doc/paml/examples/mtCDNA/mtCDNAmam.nuc.gz
/usr/share/doc/paml/examples/mtCDNA/mtCDNAmam.trees
/usr/share/doc/paml/examples/mtCDNA/mtCDNApri.aa.gz
/usr/share/doc/paml/examples/mtCDNA/mtCDNApri.nuc.gz
/usr/share/doc/paml/examples/mtCDNA/mtCDNApri.trees
/usr/share/doc/paml/examples/mtCDNAape/2s.trees
/usr/share/doc/paml/examples/mtCDNAape/OmegaAA.dat
/usr/share/doc/paml/examples/mtCDNAape/README.txt
/usr/share/doc/paml/examples/mtCDNAape/codeml.HC.ctl
/usr/share/doc/paml/examples/mtCDNAape/codeml.ctl
/usr/share/doc/paml/examples/mtCDNAape/mtCDNA.HC.txt.gz
/usr/share/doc/paml/examples/mtCDNAape/mtCDNAape.trees
/usr/share/doc/paml/examples/mtCDNAape/mtCDNAape.txt.gz

Changelog

2018-04-27 - Andreas Tille <tille@debian.org>
paml (4.9h+dfsg-1) unstable; urgency=medium
* New upstream version
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
2018-02-28 - Andreas Tille <tille@debian.org>
paml (4.9g+dfsg-3) unstable; urgency=medium
* Really enable arch=all build
Closes: 890591
2018-02-16 - Andreas Tille <tille@debian.org>
paml (4.9g+dfsg-2) unstable; urgency=medium
* Do not fail with arch=all build
Closes: #890591
2018-02-16 - Andreas Tille <tille@debian.org>
paml (4.9g+dfsg-1) unstable; urgency=medium
* New upstream version (upstream fixed format security issue)
* Standards-Version: 4.1.3
* debhelper 11
* do not parse d/changelog
2017-03-17 - Andreas Tille <tille@debian.org>
paml (4.9e+dfsg-1) unstable; urgency=medium
* This new upstream version is now covered by a free license and can
be released to main
2016-09-12 - Andreas Tille <tille@debian.org>
paml (4.9c+dfsg-1) unstable; urgency=medium
* New upstream version
* Homepage now states GPL-v3
* Moved packaging to Git
* Use new uscan options in watch file
* cme fix dpkg-control
* Removed *.pdf files since there is no source for theses files
* Add clean target to upstream Makefile
* *.ctl files are pointing to existing data files in /usr/lib/paml/data
* *.ctl files are obtained from /etc/paml if there is no such file in
current dir
* Fix permissions
2014-07-30 - Andreas Tille <tille@debian.org>
paml (4.8+dfsg-1) unstable; urgency=medium
* New upstream version
* d/rules: Adapt get-orig-source to new uscan syntax
* d/watch: uversionmangle to get correct download file name
* d/README.*: Updated
* d/control:
- Priority: optional
- cme fix dpkg-control
- XS-Autobuild: yes
* d/patches/fix_format_security.patch: Fix some format security issues
2013-08-08 - Andreas Tille <tille@debian.org>
paml (4.7-1) unstable; urgency=low
* New upstream version
* debian/control:
- cme fix dpkg-control
- use anonscm in Vcs fields
* debian/rules: provide get-orig-source target to make use of new uscan
to remove windows binaries
2012-05-15 - Andreas Tille <tille@debian.org>
paml (4.5-1) unstable; urgency=low
[ Pjotr Prins ]
* Improved long description.
[ Andreas Tille ]
* New upstream version
* Fixed watch file
* debian/control: Standards-Version: 3.9.3 (no changes needed)
* debian/rules: remove useless dh-make template
* debian/paml.dirs: removed because unneeded
* debian/{install,links}: install all binaries to
/usr/lib/debian-med/bin and symlink to /usr/bin with the
exception of evolver which has a name space conflict.  This
is renamed to /usr/bin/paml-evolver
Closes: #661519
* debian/{paml.docs,paml-doc.docs}:
- Adapted to new names
- do not duplicate the same files into both packages (paml and
paml-doc)
* debian/profile.d/paml: Set PATH to find paml executables under
their expected names
* debian/README.Debian: Document the name space conflict solution
* debian/upstream: Citation information
* debhelper 9 (control+compat)
* debian/patches/hardening.patch: Enable propagation of hardening
flags
2011-09-30 - Charles Plessy <plessy@debian.org>
paml (4.4e-1) unstable; urgency=low
* Team upload.
* New upstream release.
* Upload to unstable (Closes: #643843).
* Corrected debian/watch for downloading sources with uscan.
* Removed links to inexsistant Git repositories in debian/README.source.
* Corrected VCS URLs (debian/control).
* Conforms to Policy 3.9.2 (debian/control, no other changes needed).
* Use Debhelper 8 (debian/control, debian/compat).
* Converted debian/copyright to machine readable format version 1.0.
* Compress binary packages with xz.

See Also

Package Description
paml_4.9h+dfsg-1_amd64.deb Phylogenetic Analysis by Maximum Likelihood (PAML)
pamtester_0.1.2-4_amd64.deb utility program to test the PAM facility
pamu2fcfg_1.0.7-1_amd64.deb universal 2nd factor (U2F) PAM module command-line helper tool
pan_0.145-1_amd64.deb newsreader based on GTK2, which looks like Forte Agent
pandoc-citeproc-preamble_1.2.3_amd64.deb insert a preamble before pandoc-citeproc's bibliography
pandoc-citeproc_0.14.3.1-4build1_amd64.deb Pandoc support for Citation Style Language - tools
pandoc-data_2.2.1-3build1_all.deb general markup converter - data files
pandoc-sidenote_0.19.0.0-2build1_amd64.deb footnotes-to-sidenotes converter for Pandoc
pandoc_2.2.1-3build1_amd64.deb general markup converter
pandora-build_0.171.1-0ubuntu2_all.deb autotools made better, faster stronger
pandorafms-agent_4.1-1_all.deb Pandora FMS - The Flexible Monitoring System (agent)
pango1.0-tests_1.42.4-6_amd64.deb Layout and rendering of internationalized text - installed tests
pangoterm_0~bzr607-2_amd64.deb GTK/Pango-based terminal
pangzero_1.4.1+git20121103-4_all.deb action game that involves popping balloons with a harpoon
panko-api_6.0.0-0ubuntu1_all.deb Event storage dispatcher for Ceilometer
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