GNU bug report logs - #56999
Add phyml package tools.

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 56999 <at> debbugs.gnu.org
Subject: [bug#56999] [PATCH 1/4] gnu: Add phyml.
Date: Mon, 08 Aug 2022 10:09:05 +0200

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> 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.

-- 
Ricardo

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