AlignIO

AlignIO is a submodule of Biopython that provides input and output facilities for biological sequence alignments. It enables reading, writing, and converting alignments between a variety of common file formats and returning them as standard Python objects suitable for downstream analysis.

AlignIO represents alignments as MultipleSeqAlignment objects, which consist of a collection of SeqRecord entries aligned to the same length. Each SeqRecord retains essential metadata such as an identifier and description, while the alignment stores the aligned sequences with gaps indicated by the alignment characters.

Commonly used operations include reading a single alignment from a file, parsing multiple alignments from a stream, and writing an alignment to a chosen format. The module provides functions such as read, parse, write, and convert to facilitate these tasks, enabling easy workflow integration with other Biopython components.

Supported formats include Clustal, FASTA, PHYLIP, Nexus, Stockholm, MAF and others. Alignment data can be interconverted, enabling compatibility with external tools and analysis pipelines. The module also exposes alignment-length and sequence-count information through the standard methods on the alignment object, aiding quick inspection of results.

In Biopython workflows, AlignIO is often used alongside sequence and phylogeny components to prepare alignments for phylogenetic analysis, visualization, or downstream processing. It serves as a versatile bridge for handling alignment data generated by various alignment tools and for preparing data for multiple analytical steps.

See also Biopython, Bio.SeqRecord, Bio.Align, and related data-handling modules for broader context and integration with other bioinformatics tasks.