# Bio Alignment Io

Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO.

- Repository: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills (3090 stars)
- Category: Writing
- License: see repository
- Last updated: 2026-07-21
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-alignment-io -g -a claude-code -y`
Codex: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-alignment-io -g -a codex -y`
Cursor: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-alignment-io -g -a cursor -y`
Gemini CLI: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-alignment-io -g -a gemini-cli -y`

## 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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

## 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.

```python
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).

The rest: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/blob/HEAD/skills/bio-alignment-io/SKILL.md