From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <56999@debbugs.gnu.org>
Cc: rekado@elephly.net
Subject: [bug#56999] [PATCH 1/4] gnu: Add phyml.
Date: Fri, 5 Aug 2022 11:33:03 +0200 [thread overview]
Message-ID: <20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <398fc66441a34468a7c66370abb8f923@mdc-berlin.de>
* 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
next prev parent reply other threads:[~2022-08-05 9:35 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-08-05 9:14 [bug#56999] Add phyml package tools MadalinIonel.Patrascu
[not found] ` <handler.56999.B.165969091927817.ack@debbugs.gnu.org>
2022-08-05 9:29 ` [bug#56999] [ext] bug#56999: Acknowledgement (Add phyml package tools.) MadalinIonel.Patrascu
2022-08-08 10:35 ` Ricardo Wurmus
2022-10-31 20:47 ` bug#56999: Add phyml package tools Ricardo Wurmus
2022-08-05 9:33 ` Mădălin Ionel Patrașcu [this message]
2022-08-05 9:33 ` [bug#56999] [PATCH 2/4] gnu: Add phyml-mpi Mădălin Ionel Patrașcu
2022-08-05 9:33 ` [bug#56999] [PATCH 3/4] gnu: Add phyml-phyrex Mădălin Ionel Patrașcu
2022-08-05 9:33 ` [bug#56999] [PATCH 4/4] nu: Add phyml-rf Mădălin Ionel Patrașcu
2022-08-08 8:09 ` [bug#56999] [PATCH 1/4] gnu: Add phyml Ricardo Wurmus
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