Source: maffilter Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Julien Dutheil , Pranav Ballaney Section: science Priority: optional Build-Depends: debhelper-compat (= 13), cmake, texinfo, libbpp-phyl-omics-dev, libboost-iostreams-dev, zlib1g-dev, libbz2-dev Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/maffilter Vcs-Git: https://salsa.debian.org/med-team/maffilter.git Homepage: https://jydu.github.io/maffilter/ Rules-Requires-Root: no Package: maffilter Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: maffilter-examples Description: process genome alignment in the Multiple Alignment Format MafFilter applies a series of "filters" to a MAF file, in order to clean it, extract data and computer statistics while keeping track of the associated meta-data such as genome coordinates and quality scores. . * It can process the alignment to remove low-quality / ambiguous / masked regions. * It can export data into a single or multiple alignment file in format such as Fasta or Clustal. * It can read annotation data in GFF or GTF format, and extract the corresponding alignment. * It can perform sliding windows calculations. * It can reconstruct phylogeny/genealogy along the genome alignment. * It can compute population genetics statistics, such as site frequency spectrum, number of fixed/polymorphic sites, etc. Package: maffilter-examples Architecture: all Depends: ${misc:Depends} Enhances: maffilter Multi-Arch: foreign Description: process genome alignment in the Multiple Alignment Format (example data) MafFilter applies a series of "filters" to a MAF file, in order to clean it, extract data and computer statistics while keeping track of the associated meta-data such as genome coordinates and quality scores. . * It can process the alignment to remove low-quality / ambiguous / masked regions. * It can export data into a single or multiple alignment file in format such as Fasta or Clustal. * It can read annotation data in GFF or GTF format, and extract the corresponding alignment. * It can perform sliding windows calculations. * It can reconstruct phylogeny/genealogy along the genome alignment. * It can compute population genetics statistics, such as site frequency spectrum, number of fixed/polymorphic sites, etc. . This package provides example data for maffilter.