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[bug#56999] [PATCH 1/4] gnu: Add phyml.

From: Ricardo Wurmus
Subject: [bug#56999] [PATCH 1/4] gnu: Add phyml.
Date: Mon, 08 Aug 2022 10:09:05 +0200
User-agent: mu4e 1.8.7; emacs 28.1

Mădălin Ionel Patrașcu <> writes:

> * gnu/packages/bioinformatics.scm (phyml): New variable.

Thanks for the patch.

> +     "@code{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
> +with efficient options to search the space of phylogenetic tree topologies.  
> @code{
> +PhyTime} is another tool in the @code{PhyML} package that focuses on 
> divergence
> +date estimation in a Bayesian setting.  The main strengths of @code{PhyTime} 
> lie
> +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, code{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.
> +@code{PhyREX} can be used to estimate population densities and rates of 
> dispersal.
> +Its output can be processed by treeannotator (from the @code{BEAST} package) 
> as
> +well as @code{SPREAD}.")

The description mentions PhyTime and PhyREX, neither of which are
included in this package.  I’ll try to integrate this package with
the definitions of phyml-mpi, phyml-phyrex, and phyml-rf that you’ve
sent here.


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