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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.
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