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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=PgSptdEB; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 7.19 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=PgSptdEB; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 075649AFD X-Spam-Score: 7.19 X-Migadu-Scanner: scn1.migadu.com X-TUID: qeaURZeB1dwq * gnu/packages/bioinformatics.scm (phyml): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 00238531db..fa91f48569 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9068,6 +9068,43 @@ (define-public phylip programs for inferring phylogenies (evolutionary trees).") (license license:bsd-2))) +(define-public phyml + (package + (name "phyml") + (version "3.3.20220408") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/stephaneguindon/phyml") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03hdqmnsgnzkcrp9r9ajdfkj33jgq4b86kra8ssjlrph65y344sa")))) + (build-system gnu-build-system) + (native-inputs + (list automake + autoconf)) + (home-page "https://github.com/stephaneguindon/phyml") + (synopsis "Programs for working on SAM/BAM files") + (description + "@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}.") + (license license:gpl3))) + (define-public imp (package (name "imp") base-commit: 47a38d09696b309f6174b585465e621352444ddb -- 2.37.1