bio-alignment-msa-statistics SKILL.md skillA
bio-alignment-msa-statistics from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-alignment-msa-statistics@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-alignment-msa-statistics/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 23,394 bytes
- Repository stars
- 662
- License
- MIT
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility Reference examples tested with: BioPython 1.83+, numpy 1.26+ 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. # MSA Statistics Calculate sequence identity, conservation scores, substitution counts, and other alignment metrics. ## Required Import **Goal:** Load modules for alignment I/O, substitution scoring, and statistical calculations. **Approach:** Import AlignIO for reading alignments, Counter for column analysis, numpy for matrix operations, and math for entropy calculations. ```python from Bio import AlignIO from Bio.Align import substitution_matrices from collections import Counter import numpy as np import math ``` ## Pairwise Identity **"Calculate percent identity"** -> Compute the fraction of identical aligned residues between sequence pairs. **Goal:** Measure sequence similarity as percent identity for individual pairs or across all sequences in an alignment. …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-alignment-msa-statistics@sha256:02bb7d9ebe8437e6The line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_dbrdifcbec43mmai)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_dbrdifcbec43mmai GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-alignment-msa-statistics GET https://markdownregistry.com/api/v1/blob/02bb7d9ebe8437e6bcdb182e409c383730f1925ed9d49b93f56ed7fea7ae88a8
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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