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 skills add PKU-YuanGroup/OpenAI4S --skill bio-alignment-pairwise-alignmentgit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote 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/pku-yuangroup/openai4s/bio-alignment-pairwise-alignment)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-pairwise-alignment"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-pairwise-alignment/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-pairwise-alignment"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-pairwise-alignment.svg" alt="Reviewed on agentmods" width="80" 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 5.1 | $0.00052 | $0.05529 |
| Opus 5 | $0.00026 | $0.02764 |
| Sonnet 5 | $0.00010 | $0.01106 |
| Haiku 4.5 | $0.00005 | $0.00553 |
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 10d 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.
This is a copy
97% identical to bio-alignment-pairwise — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 410 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.
- 10d ago First seen · 410 lines · 52 tokens per session scan A 84bcd1577bf1
bio-alignment-pairwise is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (399 stars, last pushed yesterday), licensed MIT. It adds 52 tokens to every session and 5,529 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. It is 97% identical to bio-alignment-pairwise, differing in 12 lines, and is treated as a copy.
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