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