Paquet : prottest (3.4.2+dfsg-8)

[ Paquet source : prottest  ]

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.

Autres paquets associés à prottest

• dep: alter-sequence-alignment

  environnement de transformation d'alignements de séquences génomiques

• dep: java-wrappers

  enveloppeurs pour des exécutables Java

• dep: libbetter-appframework-java

  Better Swing Application Framework Java –⋅bibliothèque

• dep: libmpj-java

  Java library for parallel applications for multicore processors and clusters

• dep: libpal-java

  Phylogenetic Analysis Library

• dep: phyml

  estimation phylogénétique utilisant la probabilité maximale

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Architecture	Taille du paquet	Espace occupé une fois installé	Fichiers
all	341,2 ko	497,0 ko	[liste des fichiers]