パッケージ: prottest (3.4.2+dfsg-5)
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.
その他の prottest 関連パッケージ
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- dep: alter-sequence-alignment
- genomic sequences ALignment Transformation EnviRonment
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- dep: java-wrappers
- wrappers for java executables
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- dep: libbetter-appframework-java
- Java Better Swing Application Framework (library)
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- dep: libmpj-java
- Java library for parallel applications for multicore processors and clusters
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- dep: libpal-java
- Phylogenetic Analysis Library
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- dep: phyml
- Phylogenetic estimation using Maximum Likelihood