prottest_3.4.1+dfsg-2_all.deb


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Description

prottest - selection of best-fit models of protein evolution

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe amd64
Package name: prottest
Package version: 3.4.1+dfsg
Package release: 2
Package architecture: all
Package type: deb
Installed size: 904 B
Download size: 246.40 KB
Official Mirror: archive.ubuntu.com
PROTTEST (ModelTest's relative) is a program for selecting the model of protein evolution that best fits a given set of sequences (alignment). This java program is based on the Phyml program (for maximum likelihood calculations and optimization of parameters) and uses the PAL library as well. Models included are empirical substitution matrices (such as WAG, LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam, MtArt, HIVb, and HIVw) that indicate relative rates of amino acid replacement, and specific improvements (+I:invariable sites, +G: rate heterogeneity among sites, +F: observed amino acid frequencies) to account for the evolutionary constraints impossed by conservation of protein structure and function. ProtTest uses the Akaike Information Criterion (AIC) and other statistics (AICc and BIC) to find which of the candidate models best fits the data at hand.

Alternatives

    Download

    Source package: prottest

    Install Howto

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

    Files

    • /etc/prottest/prottest.properties
    • /usr/bin/prottest
    • /usr/share/doc/prottest/README.Debian
    • /usr/share/doc/prottest/README.gz
    • /usr/share/doc/prottest/changelog.Debian.gz
    • /usr/share/doc/prottest/copyright
    • /usr/share/doc/prottest/examples/HIV1.2008.pol.nex
    • /usr/share/doc/prottest/examples/COX2_PF0016/alignment
    • /usr/share/doc/prottest/examples/COX2_PF0016/tree
    • /usr/share/doc/prottest/examples/Ribosomal_L5_PF00673/alignment
    • /usr/share/doc/prottest/examples/Ribosomal_L5_PF00673/tree
    • /usr/share/java/prottest.jar
    • /usr/share/man/man1/prottest.1.gz
    • /usr/share/prottest/examples
    • /usr/share/prottest/prottest-3.4.1.jar
    • /usr/share/prottest/prottest.jar
    • /usr/share/prottest/prottest.properties
    • /usr/share/prottest/models/FLU

    Changelog

    2015-11-30 - Andreas Tille <tille@debian.org> prottest (3.4.1+dfsg-2) unstable; urgency=medium * Depends: phyml

    2015-10-26 - Andreas Tille <tille@debian.org> prottest (3.4.1+dfsg-1) unstable; urgency=medium *Initial release (Closes: #802325)

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