slackbuilds/academic/PhyML
Heinz Wiesinger 63daf9f79a All: Support $PRINT_PACKAGE_NAME env var
Signed-off-by: Heinz Wiesinger <pprkut@slackbuilds.org>
2021-07-17 21:55:09 +02:00
..
PhyML.SlackBuild All: Support $PRINT_PACKAGE_NAME env var 2021-07-17 21:55:09 +02:00
PhyML.info academic/PhyMLR: Updated for version 3.3.20200621. 2020-09-15 08:26:50 +07:00
README academic/PhyML: Updated for version 3.3.20170530. 2017-10-11 06:19:45 +07:00
References academic/PhyML: Updated for version 20131112. 2013-12-14 10:53:05 -06:00
slack-desc academic/PhyML: Updated for version 3.3.20170530. 2017-10-11 06:19:45 +07:00

README

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).

This also builds MPI (using multiple processors) version of PhyML, which
requires 'openmpi'. Other additional programs built by the script are
Phyrex and PhyTime. If you do not want them to be built in the package,
check the SlackBuild script.

For details and citation
New Algorithms and Methods to Estimate Maximum-Likelihood
Phylogenies: Assessing the Performance of PhyML 3.0. Guindon S.,
Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O.
Systematic Biology, 59(3):307-21, 2010.