API Reference

Bindings to FAMSA, an algorithm for fast multiple sequence alignments.

References

  • Deorowicz, S., Debudaj-Grabysz, A., Gudyś, A. (2016) FAMSA: Fast and accurate multiple sequence alignment of huge protein families. Scientific Reports, 6, 33964. doi:10.1038/srep33964.

Aligner

pyfamsa.Aligner

A single FAMSA aligner.

Sequence

pyfamsa.Sequence

A digitized sequence.

Alignment

pyfamsa.Alignment

An alignment, stored as a list of GappedSequence objects.

pyfamsa.GappedSequence

A gapped sequence, storing a single row in an alignment.

GuideTree

pyfamsa.GuideTree

A guide tree generated from several sequences.