Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/gptomics/bioskills/pairwise-alignmentnpx skills add GPTomics/bioSkills --skill pairwise-alignmentgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/gptomics/bioskills/pairwise-alignment)<a href="https://agentmods.dev/skills/gptomics/bioskills/pairwise-alignment"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/pairwise-alignment.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00052 | $0.05456 |
| Opus 5 | $0.00026 | $0.02728 |
| Sonnet 5 | $0.00010 | $0.01091 |
| Haiku 4.5 | $0.00005 | $0.00546 |
Grade A, and why
bio-alignment-pairwise scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 3d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
Copies of this mod
1 near-identical copy found in the catalogue:
- bio-alignment-pairwise — 97% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 402 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: BioPython 1.83+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(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) orwater(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.
from Bio.Align import PairwiseAligner
from Bio.Seq import Seq
from Bio import SeqIO
Pairwise Library Selection
Bio.Align.PairwiseAligner is the right default for interactive use, scripting, and pair sizes up to a few thousand residues, but it is not the fastest or most scalable option. For high-throughput screens, very long sequences, or production pipelines, switch to a SIMD-accelerated or specialised library.
| Library | Speed vs Bio.Align | Alphabet | Scoring | Vectorization | When to use |
|---|---|---|---|---|---|
Bio.Align.PairwiseAligner (BioPython) |
1x baseline | DNA / RNA / protein | Matrix + affine | C-backed Gotoh | Default, <10 kb pairs, interactive use |
parasail (Daily 2016 BMC Bioinf) |
10-100x | DNA / protein | Matrix + affine | SSE / AVX SIMD | High-throughput SW or NW; benchmark loops |
edlib (Sosic & Sikic 2017 Bioinf) |
100-1000x | DNA only | Edit distance only | Bit-parallel Myers | Read mapping, k-mer search, primer placement |
pywfa / WFA2 (Marco-Sola 2021 Bioinformatics 37:456; BiWFA: Marco-Sola 2023 Bioinformatics 39:btad074) |
Best for low-divergence | DNA | Matrix + affine | Wavefront, O(s) memory | Long, near-identical sequences (>10 kb, <5% diverged) |
mappy / minimap2 (Li 2018 Bioinf) |
Production reads-to-genome | DNA | Chain + base-level | k-mer chain | Long-read mapping, splice-aware DNA |
Bio.pairwise2 |
DEPRECATED | -- | -- | -- | Migrate to PairwiseAligner (deprecated in BioPython 1.80; not yet removed; migrate proactively) |
EMBOSS needle / water |
~Bio.Align | DNA / protein | Matrix + affine | None | Reproducibility, audit trails (fixed, documented default parameters) |
What ships with it
6 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 3d ago First seen · 402 lines · 52 tokens per session scan A 7d4e9c3aebb3
bio-alignment-pairwise is a skill published in the GitHub repository GPTomics/bioSkills (1,198 stars, last pushed 19d ago), licensed MIT. It adds 52 tokens to every session and 5,456 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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chat-perf
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Use when creating or changing VS Code chat pet sprite art, sprite sheets, state animations, eye treatments, Stable/Insiders variants, or pet transitions under src/vs/workbench/contrib/chat/browser/widget/media/chatPet.
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