API Reference#

Alignment#

`pytrimal.Alignment`	A multiple sequence alignment.
`pytrimal.TrimmedAlignment`	A multiple sequence alignment that has been trimmed.
`pytrimal.AlignmentResidues`	A read-only view over the residues of an alignment.
`pytrimal.AlignmentSequences`	A read-only view over the sequences of an alignment.

`pytrimal.BaseTrimmer`	A sequence alignment trimmer.
`pytrimal.AutomaticTrimmer`	A sequence alignment trimmer with automatic parameter detection.
`pytrimal.ManualTrimmer`	A sequence alignment trimmer with manually defined thresholds.
`pytrimal.RepresentativeTrimmer`	A sequence alignment trimmer for selecting representative sequences.
`pytrimal.OverlapTrimmer`	A sequence alignment trimmer for overlap blocks.

A similarity matrix for biological sequence characters.