/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

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).

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

**Goal:** Save alignment data to files in standard formats for downstream tools or archival.

**Approach:** Use `AlignIO.write()` with the target format specifier, supporting single or multiple alignments and file handles.

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

**"Convert alignment format"** → Transform an alignment file from one format to another (e.g., Clustal to PHYLIP).

**Goal:** Convert alignment files between formats for compatibility with different analysis tools.

**Approach:** Use `AlignIO.convert()` for direct one-step conversion, or read-modify-write for cases requiring intermediate manipulation.

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

**Goal:** Navigate and extract data from alignment objects including sequences, columns, and slices.

**Approach:** Use iteration, indexing, and column slicing on the alignment object.

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

**Goal:** Build an alignment object from sequences defined in code rather than read from a file.

**Approach:** Construct SeqRecord objects with gap characters and wrap them in a MultipleSeqAlignment.

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'),