bio-alignment-msa-statistics
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill msa-statistics --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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. **Approach:** Count ma
- Version Compatibility
- Required Import
- Pairwise Identity
- Percent Identity Definitions
- Calculate Identity Between Two Sequences
- Identity Matrix for All Sequences
- Conservation Scoring Methods
- Conservation Score
- Per-Column Conservation
- Average Conservation Across Alignment
- Conservation Profile
- Capra-Singh Jensen-Shannon Divergence
- Substitution Counts
- Count Substitutions from Alignment
modeltest-ng -i alignment.fasta -d nt -t ml modeltest-ng -i alignment.fasta -d aa -t ml -p 4
What does the bio-alignment-msa-statistics skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill msa-statistics --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.