bio-alignment-io

Required Import

Goal: Load modules for reading, writing, and manipulating multiple sequence alignments.

Approach: Import AlignIO for file I/O and supporting classes for programmatic alignment construction.

Supported Formats

Format	Extension	Read	Write	Description
clustal	.aln	Yes	Yes	Clustal W/X output
fasta	.fasta, .fa	Yes	Yes	Aligned FASTA
phylip	.phy	Yes	Yes	Interleaved PHYLIP
phylip-sequential	.phy	Yes	Yes	Sequential PHYLIP
phylip-relaxed	.phy	Yes	Yes	PHYLIP with long names
stockholm	.sto, .stk	Yes	Yes	Pfam/Rfam annotated
nexus	.nex	Yes	Yes	NEXUS format
emboss	.txt	Yes	No	EMBOSS tools output
fasta-m10	.txt	Yes	No	FASTA -m 10 output
maf	.maf	Yes	Yes	Multiple Alignment Format
mauve	.xmfa	Yes	No	progressiveMauve output
msf	.msf	Yes	No	GCG MSF format

Reading Alignments

"Read an alignment file" → Parse an alignment file into an alignment object with sequences and metadata accessible.

Goal: Load alignment data from files in various formats (Clustal, PHYLIP, Stockholm, FASTA).

Approach: Use AlignIO.read() for single-alignment files or AlignIO.parse() for files containing multiple alignments.