mirror of
https://git.FreeBSD.org/ports.git
synced 2024-12-22 04:17:44 +00:00
21 lines
1.3 KiB
Plaintext
21 lines
1.3 KiB
Plaintext
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). PhyML was designed to process moderate to large data sets. In
|
|
theory, alignments with up to 4,000 sequences 2,000,000 character-long
|
|
can analyzed. In practice however, the amount of memory required to
|
|
process a data set is proportional of the product of the number of
|
|
sequences by their length. Hence, a large number of sequences can only
|
|
be processed provided that they are short. Also, PhyML can handle long
|
|
sequences provided that they are not numerous. With most standard
|
|
personal computers, the "comfort zone" for PhyML generally lies around 3
|
|
to 500 sequences less than 2,000 character long.
|
|
|
|
WWW: https://github.com/stephaneguindon/phyml
|