19 lines
1.2 KiB
Text
19 lines
1.2 KiB
Text
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PhyML is a software that estimates maximum likelihood phylogenies from
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alignments of nucleotide or amino acid sequences. It provides a wide range of
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options that were designed to facilitate standard phylogenetic analyses. The
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main strengths of PhyML lies in the large number of substitution models coupled
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to various options to search the space of phylogenetic tree topologies, going
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from very fast and efficient methods to slower but generally more accurate
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approaches. It also implements two methods to evaluate branch supports in a
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sound statistical framework (the non-parametric bootstrap and the approximate
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likelihood ratio test). PhyML was designed to process moderate to large data
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sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long
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can analyzed. In practice however, the amount of memory required to process a
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data set is proportional of the product of the number of sequences by their
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length. Hence, a large number of sequences can only be processed provided that
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they are short. Also, PhyML can handle long sequences provided that they are
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not numerous. With most standard personal computers, the "comfort zone" for
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PhyML generally lies around 3 to 500 sequences less than 2,000 character long.
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WWW: http://code.google.com/p/phyml/
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