Пакет: prottest (3.4.2+dfsg-8)

[ Источник: 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.

Другие пакеты, относящиеся к prottest

• dep: alter-sequence-alignment

  genomic sequences ALignment Transformation EnviRonment

• dep: java-wrappers

  обертки для исполняемых java

• dep: libbetter-appframework-java

  Java Better Swing Application Framework (library)

• dep: libmpj-java

  Java library for parallel applications for multicore processors and clusters

• dep: libpal-java

  Phylogenetic Analysis Library

• dep: phyml

  Phylogenetic estimation using Maximum Likelihood

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