Version Compatibility

Reference examples tested with: BioPython 1.83+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Alignment File I/O

Read, write, and convert multiple sequence alignment files in various formats.

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.

from Bio import AlignIO
from Bio.Align import MultipleSeqAlignment
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq

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).