Scan contig files against PubMLST typing schemes

Mass screening of contigs for antibiotic resistance genes

phase genomic variants using DNA sequencing reads (haplotype assembly)

ARIBA: Antibiotic Resistance Identification By Assembly

peddy compares familial-relationships and sexes as reported in a PED/FAM file with those inferred from a VCF.

Efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites

is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).