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26 lines
1.3 KiB
Text
26 lines
1.3 KiB
Text
PhyML is a software that estimates maximum likelihood phylogenies
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from alignments of nucleotide or amino acid sequences. It provides a
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wide range of options that were designed to facilitate standard
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phylogenetic analyses. The main strengths of PhyML lies in the large
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number of substitution models coupled to various options to search
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the space of phylogenetic tree topologies, going from very fast and
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efficient methods to slower but generally more accurate approaches.
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It also implements two methods to evaluate branch supports in a sound
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statistical framework (the non-parametric bootstrap and the
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approximate likelihood ratio test).
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NOTE 1: This also builds Phyrex and the MPI (using multiple processors)
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version of PhyML. The executable of the latter is called phyml-mpi and
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requires openmpi. If you do not want them to be built in the package,
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check the SlackBuild script.
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NOTE 2: PhyTime used to be part of the PhyML package. However, PhyTime
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from the latest releases of PhyML does not build anymore. meanwhile,
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PhyTime is available separately, which installs the latest version that
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builds.
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For details and citation
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New Algorithms and Methods to Estimate Maximum-Likelihood
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Phylogenies: Assessing the Performance of PhyML 3.0. Guindon S.,
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Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O.
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Systematic Biology, 59(3):307-21, 2010.
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