Bug#802325: ITP: prottest -- selection of best-fit models of protein evolution
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>
* Package name : prottest
Version : 3.4
Upstream Author : Diego Darriba <diegodl84@gmail.com>
* URL : https://github.com/ddarriba/prottest3
* License : GPL
Programming Lang: Java
Description : selection of best-fit models of protein evolution
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.
This package will be maintained by the Debian Med team at
git://anonscm.debian.org/debian-med/prottest.git
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