Alignment

class pyfamsa.Alignment

An alignment, stored as a list of GappedSequence objects.

class pyfamsa.GappedSequence

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

Internally, gapped sequences are not stored in a single string in FAMSA, but using a gap counter for each position. This allows saving a lot of memory for alignments containing lots of gaps, but adds some overhead to decode the full sequence.

id

The identifier of the gapped sequence.

Type:

bytes

sequence

The symbols of the gapped sequence as an ASCII string.

Type:

bytes