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bio-alignment-msa-statistics
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-alignment-msa-statistics
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Calculate sequence identity, conservation scores, substitution counts, and other alignment metrics.
- print(substitutions).
Source Doc
Excerpt From SKILL.md
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.
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.
Approach: Count matching non-gap positions divided by total aligned positions; optionally compute a full N-by-N identity matrix.
Conservation Score
Goal: Quantify per-column and overall alignment conservation to identify conserved and variable regions.
Approach: Calculate the fraction of the most common residue at each column, optionally ignoring gaps, and smooth with a sliding window.
Use cases
- Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- msa-parsing - Parse and manipulate alignments
- alignment-io - Read/write alignment files
- pairwise-alignment - Create and score pairwise alignments
- sequence-manipulation/sequence-properties - Sequence-level statistics
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