| Message ID | 20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de |
|---|---|
| State | New |
| Headers | show |
| Series | [bug#56999,1/4] gnu: Add phyml. | expand |
| Context | Check | Description |
|---|---|---|
| cbaines/comparison | success | View comparision |
| cbaines/git-branch | success | View Git branch |
| cbaines/applying patch | success | View Laminar job |
| cbaines/issue | success | View issue |
Mădălin Ionel Patrașcu <madalinionel.patrascu@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.
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")