maffilter

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.