Subject: [bug#57135] [PATCH] gnu: Add mrbayes.

From: Mădălin Ionel Patrașcu<[email-masked]>
Date: Thu, 11 Aug 2022 10:30:10 +0200

* gnu/packages/bioinformatics.scm (mrbayes): New variable.
---
 gnu/packages/bioinformatics.scm | 67 +++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3a40cc2281..ae362de1e7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11155,6 +11155,73 @@ (define-public mantis
       (supported-systems '("x86_64-linux"))
       (license license:bsd-3))))
 
+(define-public mrbayes
+  (package
+    (name "mrbayes")
+    (version "3.2.7a")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/NBISweden/MrBayes/")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1c4qg4wd6lhj1if5g6462pk15bhh7v84ys92sp47yih7lrkk2jd6"))))
+    (properties `((upstream-name . "MrBayes")))
+    (build-system gnu-build-system)
+    (native-inputs
+     (list automake
+           autoconf))
+    (home-page "https://github.com/NBISweden/MrBayes/")
+    (synopsis "Bayesian inference of phylogeny")
+    (description
+     "@code{MrBayes} is a program for Bayesian inference and model choice across
+a wide range of phylogenetic and evolutionary models.  @code{MrBayes} uses @dfn{
+MCMC} (Markov chain Monte Carlo) methods to estimate the posterior distribution
+of model parameters.  Program features include:
+@itemize
+@item
+analysis of nucleotide, amino acid, restriction site, and morphological data;
+@item
+mixing of data types, such as molecular and morphological characters, in a single
+analysis;
+@item
+easy linking and unlinking of parameters across data partitions;
+@item
+multiple evolutionary models, including 4x4, doublet, and codon models for
+nucleotide data and many of the standard rate matrices for amino acid data;
+@item
+estimation of positively selected sites in a fully hierarchical Bayesian framework;
+@item
+full integration of the @code{BEST} algorithms for the multi-species coalescent;
+@item
+estimation of time calibrated (clock) trees using a variety of (strict and)
+relaxed-clock models;
+@item
+support for complex combinations of positive, negative, and backbone constraints
+on topologies;
+@item
+model jumping across the @code{GTR} model space and across fixed rate matrices
+for amino acid data;
+@item
+monitoring of convergence during the analysis, and access to a wide range of
+convergence diagnostics tools after the analysis has finished;
+@item
+rich summaries of posterior samples of branch and node parameters printed to
+majority rule consensus trees in FigTree format;
+@item
+implementation of the stepping-stone method for accurate estimation of model
+likelihoods for Bayesian model choice using Bayes factors;
+@item
+ability to spread jobs over a cluster of computers using @code{MPI} (for
+Macintosh and UNIX environments only);
+@item
+support for the @code{BEAGLE} library, resulting in dramatic speedups for codon
+and amino acid models on compatible hardware (NVIDIA graphics cards);
+@end itemize")
+    (license license:gpl3)))
+
 (define-public sjcount
   ;; There is no tag for version 3.2, nor is there a release archive.
   (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")

base-commit: 6ce3e51aa876681967177812dc295c86a50d7446
-- 
2.37.1