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bio-alignment-msa-statistics
维护者 FreedomIntelligence · 最近更新 2026年4月1日
bio-alignment-msa-statistics：Calculate alignment statistics ，涵盖 sequence identity，conservation scores，substitution matrices，、 similarity metrics。 适合在comparing alignment quality，measuring sequence divergence，、 analyzing evolutionary patterns时使用。
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-alignment-msa-statistics
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- Calculate sequence identity，conservation scores，substitution counts，、 other alignment metrics。
- print(substitutions)。
原始文档
SKILL.md 摘录
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.
适用场景
- 适合在comparing alignment quality，measuring sequence divergence，、 analyzing evolutionary patterns时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- 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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