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authorPetar Petrov <ppetrov@paju.oulu.fi>2011-09-27 07:28:20 -0300
committerNiels Horn <niels.horn@slackbuilds.org>2011-09-27 07:28:20 -0300
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academic/PhyML: Updated for version 20110526.
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-PhyML is a phylogeny software based on the maximum-likelihood
-principle. Early PhyML versions used a fast algorithm to perform
-Nearest Neighbor Interchanges (NNIs), in order to improve a
-reasonable starting tree topology.
+PhyML is a software that estimates maximum likelihood phylogenies
+from alignments of nucleotide or amino acid sequences. It provides a
+wide range of options that were designed to facilitate standard
+phylogenetic analyses. The main strengths of PhyML lies in the large
+number of substitution models coupled to various options to search
+the space of phylogenetic tree topologies, going from very fast and
+efficient methods to slower but generally more accurate approaches.
+It also implements two methods to evaluate branch supports in a sound
+statistical framework (the non-parametric bootstrap and the
+approximate likelihood ratio test).
For details and citation
New Algorithms and Methods to Estimate Maximum-Likelihood