Source: phyml
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>,
           Andreas Tille <tille@debian.org>,
           Kevin Murray <spam@kdmurray.id.au>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
               pkg-config,
#               libhmsbeagle-dev [any-amd64 any-i386 arm64 armhf],
               libopenmpi-dev,
               chrpath
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/phyml
Vcs-Git: https://salsa.debian.org/med-team/phyml.git
Homepage: http://www.atgc-montpellier.fr/phyml
Rules-Requires-Root: no

Package: phyml
Architecture: any
Depends: ${shlibs:Depends},
         ${misc:Depends},
         openmpi-bin
Description: Phylogenetic estimation using Maximum Likelihood
 PhyML is a software that estimates maximum likelihood phylogenies from
 alignments of nucleotide or amino acid sequences. It provides a wide
 range of options that were designed to facilitate standard phylogenetic
 analyses. The main strengths of PhyML lies in the large number of
 substitution models coupled to various options to search the space of
 phylogenetic tree topologies, going from very fast and efficient methods
 to slower but generally more accurate approaches. It also implements
 two methods to evaluate branch supports in a sound statistical framework
 (the non-parametric bootstrap and the approximate likelihood ratio test).
 .
 PhyML was designed to process moderate to large data sets. In theory,
 alignments with up to 4,000 sequences 2,000,000 character-long can
 be analyzed. In  practice however, the amount of memory required to process
 a data set is proportional of the product of the number of sequences by their
 length. Hence, a large number of sequences can only be processed provided
 that they are short. Also, PhyML can handle long sequences provided that
 they are not numerous. With most standard personal computers, the “comfort
 zone” for PhyML generally lies around 3 to 500 sequences less than 2,000
 character long.
 .
 This package also includes PhyTime.

#Package: phyml-beagle
#Architecture: any-amd64 any-i386 arm64 armhf
#Depends: ${shlibs:Depends},
#         ${misc:Depends},
#         openmpi-bin
#Description: Phylogenetic estimation using Maximum Likelihood
# PhyML is a software that estimates maximum likelihood phylogenies from
# alignments of nucleotide or amino acid sequences. It provides a wide
# range of options that were designed to facilitate standard phylogenetic
# analyses. The main strengths of PhyML lies in the large number of
# substitution models coupled to various options to search the space of
# phylogenetic tree topologies, going from very fast and efficient methods
# to slower but generally more accurate approaches. It also implements
# two methods to evaluate branch supports in a sound statistical framework
# (the non-parametric bootstrap and the approximate likelihood ratio test).
# .
# PhyML was designed to process moderate to large data sets. In theory,
# alignments with up to 4,000 sequences 2,000,000 character-long can
# be analyzed. In  practice however, the amount of memory required to process
# a data set is proportional of the product of the number of sequences by their
# length. Hence, a large number of sequences can only be processed provided
# that they are short. Also, PhyML can handle long sequences provided that
# they are not numerous. With most standard personal computers, the “comfort
# zone” for PhyML generally lies around 3 to 500 sequences less than 2,000
# character long.
# .
# This package contains the hmsbeagle optimisation.