prottest_3.4.2+dfsg-2_all.deb


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Description

prottest - selection of best-fit models of protein evolution

Property Value
Distribution Ubuntu 17.10 (Artful Aardvark)
Repository Ubuntu Universe i386
Package name prottest
Package version 3.4.2+dfsg
Package release 2
Package architecture all
Package type deb
Installed size 494 B
Download size 337.78 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

Package Version Architecture Repository
prottest_3.4.2+dfsg-2_all.deb 3.4.2+dfsg all Ubuntu Universe
prottest - - -

Requires

Name Value
alter-sequence-alignment -
java-wrappers -
libmpj-java -
libpal-java -
phyml -

Download

Type URL
Binary Package prottest_3.4.2+dfsg-2_all.deb
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

Path
/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-3.4.2.jar
/usr/share/prottest/prottest.jar
/usr/share/prottest/prottest.properties
/usr/share/prottest/models/FLU

Changelog

2016-05-11 - Andreas Tille <tille@debian.org>
prottest (3.4.2+dfsg-2) unstable; urgency=medium
* Adapt to libmpj-java settings
* Fix wrapper scripts
2016-05-10 - Andreas Tille <tille@debian.org>
prottest (3.4.2+dfsg-1) unstable; urgency=medium
* New upstream version
* Use repack and compress option in watch file
* Drop libnb-absolutelayout-java Build-Depends
* Cleanup d/copyright from files removed upstream
* cme fix dpkg-control
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)

See Also

Package Description
prov-tools_1.5.0-2_all.deb tools for prov
prover9-doc_0.0.200902a-2_all.deb documentation for Prover9 and associated programs
prover9-mace4_0.5.dfsg-3_all.deb GUI for Prover9 and Mace4
prover9_0.0.200911a-2.1_i386.deb theorem prover and countermodel generator
proxsmtp_1.10-2.1_i386.deb multi purpose SMTP Proxy
proxychains_3.1-7_all.deb proxy chains - redirect connections through proxy servers
proxycheck_0.49a-5_i386.deb checks existence of open proxy
proxytrack_3.49.2-1_i386.deb Build HTTP Caches using archived websites copied by HTTrack
proxytunnel_1.9.0+svn250-6_i386.deb Create tcp tunnels trough HTTPS proxies, for using with SSH
prt_0.19-2_all.deb Command line Perl Refactoring Tool
pry_0.10.3-2_all.deb powerful irb alternative and runtime developer console
ps-watcher_1.08-8_all.deb monitoring a system via ps-like commands
ps2eps_1.68+binaryfree-2_i386.deb convert PostScript to EPS (Encapsulated PostScript) files
psad_2.4.3-1.1_i386.deb Port Scan Attack Detector
pscan_1.2-9_i386.deb Format string security checker for C files
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