bio-alignment-io

name	bio-alignment-io
description	Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
tool_type	python
primary_tool	Bio.AlignIO

Alignment File I/O

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

Required Import

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

Single Alignment File

from Bio import AlignIO

alignment = AlignIO.read('alignment.aln', 'clustal')
print(f'Alignment length: {alignment.get_alignment_length()}')
print(f'Number of sequences: {len(alignment)}')

Multiple Alignments in One File

for alignment in AlignIO.parse('multi_alignment.sto', 'stockholm'):
    print(f'Alignment with {len(alignment)} sequences, length {alignment.get_alignment_length()}')

Read as List

alignments = list(AlignIO.parse('alignments.phy', 'phylip'))
print(f'Read {len(alignments)} alignments')

Writing Alignments

Write Single Alignment

AlignIO.write(alignment, 'output.fasta', 'fasta')

Write Multiple Alignments

alignments = [alignment1, alignment2, alignment3]
count = AlignIO.write(alignments, 'output.sto', 'stockholm')
print(f'Wrote {count} alignments')

Write to Handle

with open('output.aln', 'w') as handle:
    AlignIO.write(alignment, handle, 'clustal')

Format Conversion

Direct Conversion (Most Efficient)

AlignIO.convert('input.aln', 'clustal', 'output.phy', 'phylip')

With Alphabet Specification

AlignIO.convert('input.sto', 'stockholm', 'output.nex', 'nexus', molecule_type='DNA')

Manual Conversion (When Modification Needed)

alignment = AlignIO.read('input.aln', 'clustal')
# ... modify alignment ...
AlignIO.write(alignment, 'output.fasta', 'fasta')

Accessing Alignment Data

alignment = AlignIO.read('alignment.aln', 'clustal')

# Iterate over sequences
for record in alignment:
    print(f'{record.id}: {record.seq}')

# Access by index
first_seq = alignment[0]
last_seq = alignment[-1]

# Slice columns
column_slice = alignment[:, 10:20]  # Columns 10-19

# Get specific column
column = alignment[:, 5]  # Column 5 as string

Working with Alignment Objects

Get Alignment Properties

alignment = AlignIO.read('alignment.aln', 'clustal')

length = alignment.get_alignment_length()
num_seqs = len(alignment)
seq_ids = [record.id for record in alignment]

Slice Alignments

# Get subset of sequences
subset = alignment[0:5]  # First 5 sequences

# Get subset of columns
trimmed = alignment[:, 50:150]  # Columns 50-149

# Combine slicing
region = alignment[0:5, 50:150]  # 5 sequences, columns 50-149

Creating Alignments Programmatically

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

records = [
    SeqRecord(Seq('ACTGACTGACTG'), id='seq1'),
    SeqRecord(Seq('ACTGACT-ACTG'), id='seq2'),
    SeqRecord(Seq('ACTG-CTGACTG'), id='seq3'),
]
alignment = MultipleSeqAlignment(records)
AlignIO.write(alignment, 'new_alignment.fasta', 'fasta')

Format-Specific Notes

PHYLIP Format

# Standard PHYLIP (10 char names, interleaved)
alignment = AlignIO.read('file.phy', 'phylip')

# Sequential PHYLIP
alignment = AlignIO.read('file.phy', 'phylip-sequential')

# Relaxed PHYLIP (allows longer names)
alignment = AlignIO.read('file.phy', 'phylip-relaxed')

Stockholm Format (with Annotations)

alignment = AlignIO.read('pfam.sto', 'stockholm')

# Access annotations
for record in alignment:
    print(record.id, record.annotations)

Clustal Format

# Clustal preserves conservation symbols in file but not when parsed
alignment = AlignIO.read('clustal.aln', 'clustal')

Batch Processing Multiple Files

from pathlib import Path

input_dir = Path('alignments/')
output_dir = Path('converted/')

for input_file in input_dir.glob('*.aln'):
    alignment = AlignIO.read(input_file, 'clustal')
    output_file = output_dir / f'{input_file.stem}.fasta'
    AlignIO.write(alignment, output_file, 'fasta')

Alternative: Bio.Align Module I/O

The newer Bio.Align module provides its own I/O functions that return Alignment objects (instead of MultipleSeqAlignment). These support additional formats and provide access to modern alignment features.

from Bio import Align

# Read single alignment (returns Alignment object)
alignment = Align.read('alignment.aln', 'clustal')

# Parse multiple alignments
for alignment in Align.parse('multi.sto', 'stockholm'):
    print(f'Alignment with {len(alignment)} sequences')

# Write alignment
Align.write(alignment, 'output.fasta', 'fasta')

When to Use Which

Use Case	Module
Legacy code, MultipleSeqAlignment needed	Bio.AlignIO
Modern features (counts, substitutions)	Bio.Align
Format conversion	Either works
Working with pairwise alignments	Bio.Align

Quick Reference: Common Operations

Task	Code
Read single alignment	AlignIO.read(file, format)
Read multiple alignments	AlignIO.parse(file, format)
Write alignment(s)	AlignIO.write(align, file, format)
Convert format	AlignIO.convert(in_file, in_fmt, out_file, out_fmt)
Get length	alignment.get_alignment_length()
Get sequence count	len(alignment)
Slice columns	alignment[:, start:end]

Common Errors

Error	Cause	Solution
ValueError: No records	Empty file	Check file path and format
ValueError: More than one record	Multiple alignments with read()	Use parse() instead
ValueError: Sequences different lengths	Invalid alignment	Ensure all sequences same length
ValueError: unknown format	Unsupported format string	Check supported formats list

Related Skills

• pairwise-alignment - Create pairwise alignments with PairwiseAligner
• msa-parsing - Analyze alignment content and annotations
• msa-statistics - Calculate conservation and identity
• sequence-io/format-conversion - Convert sequence (non-alignment) formats