Package Align

Code for dealing with sequence alignments.

One of the most important things in this module is the MultipleSeqAlignment class, used in the Bio.AlignIO module.

Submodules

Bio.Align.AlignInfo: Extract information from alignment objects.
Bio.Align.Applications: Alignment command line tool wrappers.
- Bio.Align.Applications._ClustalOmega: Command line wrapper for the multiple alignment program Clustal Omega.
- Bio.Align.Applications._Clustalw: Command line wrapper for the multiple alignment program Clustal W.
- Bio.Align.Applications._Dialign: Command line wrapper for the multiple alignment program DIALIGN2-2.
- Bio.Align.Applications._Mafft: Command line wrapper for the multiple alignment programme MAFFT.
- Bio.Align.Applications._Muscle: Command line wrapper for the multiple alignment program MUSCLE.
- Bio.Align.Applications._Prank: Command line wrapper for the multiple alignment program PRANK.
- Bio.Align.Applications._Probcons: Command line wrapper for the multiple alignment program PROBCONS.
- Bio.Align.Applications._TCoffee: Command line wrapper for the multiple alignment program TCOFFEE.
Bio.Align.Generic: Contains classes to deal with generic sequence alignment stuff not specific to a particular program or format.

Classes

MultipleSeqAlignment
Represents a classical multiple sequence alignment (MSA).