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ProtTest was the first program developed for the selection of best-fit models of protein evolution. It is an open source java program (http://darwin.uvigo.es) to find the best model of amino acid replacement for a given protein alignment. It is based on the Phyml program for the maximum likelihood (ML) optimizations, modified to support +F and four extra substitution matrices and uses the PAL library for handling protein alignments and trees.

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