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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

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

Supported Formats

Reading Alignments

Single Alignment File

Copyfrom 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

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

Read as List

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

Writing Alignments

Write Single Alignment

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

Write Multiple Alignments

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

Write to Handle

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

Format Conversion

Direct Conversion (Most Efficient)

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

With Alphabet Specification

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

Manual Conversion (When Modification Needed)

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

Accessing Alignment Data

Copyalignment = 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

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

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

Slice Alignments

Copy# 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

Copyfrom 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

Copy# 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)

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

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

Clustal Format

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

Batch Processing Multiple Files

Copyfrom 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.

Copyfrom 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

Quick Reference: Common Operations

Common Errors

Related Skills

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