bio-alignment-msa-statistics skillA
bio-alignment-msa-statistics is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns 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. …
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How to install
mdr add pku-yuangroup/openai4s/bio-alignment-msa-statistics@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-alignment-msa-statistics@sha256:02bb7d9ebe8437e6Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · 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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