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ProtTest3: HPC selection of best-fit models of protein evolution  

2012-06-15 11:26:21|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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Current version is 3.0-beta.

DOWNLOAD HERE

Online Documentation

Please report any comment or incidence in the ProtTest forum (you should be registered).


Use of ProtTest's logo kindly allowed by IconBAZAAR .


PROTTEST3 is a high-performance computing program for selecting the model of protein evolution that best fits a given set of aligned sequences. This java program uses the Phyml program (for maximum likelihood calculations and optimization of parameters) and the PAL library for handling trees, and the ALTER library for reading aligment formats. Empirical models included are as WAG, LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam, MtArt, HIVb/HIVw and FLU, plus +I:invariable sites, +G: rate heterogeneity among sites and +F: observed amino acid frequencies. ProtTest uses the Akaike Information Criterion (AIC) and other statistics (AICc, BIC and DT) to find which of the candidate models best fits the data at hand. It also implements the calculation of model-averged phylogenies.

Operative systems
ProtTest3 runs on Mac OSX (PPC / Intel), Windows and Linux.

Citation
Darriba D, Taboada GL, Doallo R, Posada D. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27: 1164-1165.

In addition, given that ProtTest uses intensively Phyml and PAL, we encourage users to cite these programs as well when using ProtTest:
- Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52: 696-704. [Phyml]
- Drummond, A., and K. Strimmer. 2001. PAL: An object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 17: 662-663. [PAL]

Contact
Correspondence about this program should be addressed to David Posada ( dposada@uvigo.es ) and ( ddarriba@udc.es )

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