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envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (mrbayes): New variable. --- gnu/packages/bioinformatics.scm | 67 +++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) base-commit: 6ce3e51aa876681967177812dc295c86a50d7446 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")