# Bio Alignment Pairwise

Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner.

- Repository: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills (3090 stars)
- Category: Engineering
- 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-pairwise -g -a claude-code -y`
Codex: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-alignment-pairwise -g -a codex -y`
Cursor: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-alignment-pairwise -g -a cursor -y`
Gemini CLI: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-alignment-pairwise -g -a gemini-cli -y`

## Description

Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.

## 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.

# Pairwise Sequence Alignment

**"Align two sequences"** → Compute an optimal alignment between a pair of sequences using dynamic programming.
- Python: `PairwiseAligner()` (BioPython Bio.Align)
- CLI: `needle` (global) or `water` (local) from EMBOSS
- R: `pairwiseAlignment()` (Biostrings)

Align two sequences using dynamic programming algorithms (Needleman-Wunsch for global, Smith-Waterman for local).

## Required Import

**Goal:** Load modules needed for pairwise alignment operations.

**Approach:** Import the PairwiseAligner class along with sequence and I/O utilities from Biopython.

```python
from Bio.Align import PairwiseAligner
from Bio.Seq import Seq
from Bio import SeqIO
```

## Core Concepts

| Mode | Algorithm | Use Case |
|------|-----------|----------|
| `global` | Needleman-Wunsch | Full-length alignment, similar-length sequences |
| `local` | Smith-Waterman | Find best matching regions, different-length sequences |

## Creating an Aligner

**Goal:** Configure a PairwiseAligner with appropriate scoring for the sequence type.

**Approach:** Instantiate PairwiseAligner with mode, scoring parameters, or a substitution matrix depending on DNA vs protein input.

```python
# Basic aligner with defaults
aligner = PairwiseAligner()

# Configure mode and scoring
aligner = PairwiseAligner(mode='global', match_score=2, mismatch_score=-1, open_gap_score=-10, extend_gap_score=-0.5)

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