HPC Module: PhyML

Synopsis

Adds PhyML software to your environment.

About This Software
Official Site	https://github.com/stephaneguindon/phyml
Tags	Phylogeny, Maximum Likelihood

Installed Versions

Version	Install Date	Default?
3.1	2019-04-10
3.3.20200621	2019-04-10
3.3.20211118	2021-11-19

Description

PhyML is a software package that uses modern statistical approaches to analyse alignments of nucleotide or amino acid sequences in a phylogenetic framework. The main tool in this package builds phylogenies under the maximum likelihood criterion. It implements a large number of substitution models coupled to efficient options to search the space of phylogenetic tree topologies. PhyTime is another tool in the PhyML package that focuses on divergence date estimation in a Bayesian setting. The main strengths of PhyTime lies in its ability to accommodate for uncertrainty in the placement of fossil calibration and the use of realistic models of rate variation along the tree. Finally, PhyREX fits the spatial-Lambda-Fleming-Viot model to geo-referenced genetic data. This model is similar to the structured coalescent but assumes that individuals are distributed along a spatial continuum rather than discrete demes. PhyREX can be used to estimate population densities and rates of dispersal. Its output can be processed by treeannotator (from the BEAST package) as well as SPREAD.

Citation(s)

If you use PhyML in your research, please cite:

• New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 S Guindon, JF Dufayard, V Lefort, M Anisimova, W Hordijk, O Gascuel Systematic Biology 59 (3), 307-321, 2010.

• Accounting for calibration uncertainty: Bayesian molecular dating as a “doubly intractable” problem S Guindon Systematic Biology 67 (4), 651–661, 2018.

• Demographic inference under the coalescent in a spatial continuum S Guindon, H Guo, D Welch Theoretical Population Biology 111, 43-50, 2016.

Category

Library	Programming	Software	SysAdmin