Source: parsnp
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>,
           Étienne Mollier <emollier@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
               dh-python,
               python3-all-dev,
               python3-setuptools,
               cython3,
               libmuscle-dev
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/parsnp
Vcs-Git: https://salsa.debian.org/med-team/parsnp.git
Homepage: https://harvest.readthedocs.org/en/latest/content/parsnp.html
Rules-Requires-Root: no

Package: parsnp
Architecture: any
Depends: ${shlibs:Depends},
         ${misc:Depends},
         ${python3:Depends},
         python3-biopython,
         python3-numpy,
         fasttree,
         harvest-tools,
         mummer,
         phipack,
         python3,
         raxml
Recommends: python3-dendropy
Description: rapid core genome multi-alignment
 Parsnp was designed to align the core genome of hundreds to thousands of
 bacterial genomes within a few minutes to few hours. Input can be both
 draft assemblies and finished genomes, and output includes variant (SNP)
 calls, core genome phylogeny and multi-alignments. Parsnp leverages
 contextual information provided by multi-alignments surrounding SNP
 sites for filtration/cleaning, in addition to existing tools for
 recombination detection/filtration and phylogenetic reconstruction.