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Source: gubbins
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-sequence-python3,
autoconf-archive,
pkgconf,
fasttree,
iqtree,
raxml,
python3-setuptools,
zlib1g-dev,
check,
python3,
python3-biopython,
python3-dendropy,
python3-reportlab,
tox <!nocheck>,
python3-scipy <!nocheck>,
python3-multiprocess <!nocheck>,
python3-wheel <!nocheck>
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/gubbins
Vcs-Git: https://salsa.debian.org/med-team/gubbins.git
Homepage: https://sanger-pathogens.github.io/gubbins/
Rules-Requires-Root: no
Package: gubbins
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
python3,
python3-pkg-resources,
raxml
# FIXME: python3-numba is disabled until version 0.59 makes it back to testing.
# Delete also remove-numba-temporarily.patch when the time comes to bring back
# numba support in gubbins.
# python3-numba
Recommends: iqtree,
fasttree
Suggests: r-base-core
Description: phylogenetic analysis of genome sequences
Gubbins supports rapid phylogenetic analysis of large samples of
recombinant bacterial whole genome sequences.
.
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide
Sequences) is an algorithm that iteratively identifies loci containing
elevated densities of base substitutions while concurrently constructing
a phylogeny based on the putative point mutations outside of these
regions. Simulations demonstrate the algorithm generates highly accurate
reconstructions under realistic models of short-term bacterial
evolution, and can be run in only a few hours on alignments of hundreds
of bacterial genome sequences.
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