phyml_20110919-1_amd64.deb


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Description

phyml - Phylogenetic estimation using Maximum Likelihood

Distribution: Debian 7 (Wheezy)
Repository: Debian Main amd64
Package name: phyml
Package version: 20110919
Package release: 1
Package architecture: amd64
Package type: deb
Installed size: 1.91 KB
Download size: 1.02 MB
Official Mirror: ftp.br.debian.org
PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the “comfort zone” for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. This pakcage also includes PhyTime.

Alternatives

Requires

    Download

    Source package: phyml

    Install Howto

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

    Files

    • /usr/bin/phyml
    • /usr/bin/phytime
    • /usr/share/doc-base/phyml
    • /usr/share/doc/phyml/changelog.Debian.gz
    • /usr/share/doc/phyml/changelog.gz
    • /usr/share/doc/phyml/copyright
    • /usr/share/doc/phyml/phyml_manual.pdf
    • /usr/share/man/man1/phyml.1.gz

    Changelog

    2011-12-05 - Charles Plessy <plessy@debian.org> phyml (2:20110919-1) unstable; urgency=low * New upstream version. * Kept manual's old name with no date (debian/docs, debian/rules). * Do not compress PDFs (debian/rules).

    2011-06-26 - Charles Plessy <plessy@debian.org> phyml (2:20110526-1) unstable; urgency=low * New upstream version. * debian/control: - Corrected VCS URLs. - Using debhelper 8 (debian/compat). - Enhances bioperl-run (that has a PhyML wrapper). - Standards-Version incremented to reflect compliance with Policy 3.9.2. * Added build-arch and build-indep targets to debian/rules. * Build and distribute PhyTime (debian/rules, debian/control).

    2011-02-14 - Andreas Tille <tille@debian.org> phyml (2:20100720-1) unstable; urgency=low * New upstream version * Fixed watch file * Standard-Version: 3.9.1 (no changes needed) * Source format 3.0 (quilt) * Wrote man page

    2010-03-07 - Charles Plessy <plessy@debian.org> phyml (2:20100123-1) unstable; urgency=low * New upstream release. [ Nelson A. de Oliveira ] * Fix watch file. * Increment the epoch number to fix a typo in the version number. [ Charles Plessy ] * Checked conformance with Policy 3.8.4 and incremented Standards-Version in debian/control to reflect this (no changes needed). * Moved the bibliographic reference from debian/reference to debian/upstream-metadata.yaml. * Adapted debian/rules to the new location of the auto(conf|make) files.

    2009-07-15 - Charles Plessy <plessy@debian.org> phyml (1:200900706-2) unstable; urgency=low * Disable parallel building, that was incorrectly supported and induced build failures by race condition (Closes: #536967).

    2009-07-11 - Charles Plessy <plessy@debian.org> phyml (1:200900706-1) unstable; urgency=low * New upstream release. * Suppressed unneeded Lintian overrides, and use ‘dh clean’ in debian/rules. * Checked conformance with Policy 3.8.2 and incremented Standards-Version in debian/control to reflect this (no changes needed). * Experimentation on the format of debian/copyright.

    2009-05-16 - Charles Plessy <plessy@debian.org> phyml (1:20090501-1) unstable; urgency=low * New upstream release clarifying the license of the documentation and switching to a versionning system that can be sorted by numerical order. * Added debian/source.lintian-overrides to indicate that the configure-generated files are deleted at cleaning time. * Using ‘dh binary-arch’ to simplify debian/rules.

    2009-05-01 - Charles Plessy <plessy@debian.org> phyml (30042009-1) unstable; urgency=low * Initial release (Closes: #517165)

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