bio-phylo-species-trees
Estimate species trees using coalescent methods including ASTRAL-III, wASTRAL, ASTRAL-Pro, SVDQuartets, and BPP. Use when multi-locus data shows gene tree discordance from incomplete lineage sorting, when in the anomaly zone where concatenation is misleading, or when computing concordance factors to assess topological support.
npx skills add BioTender-max/awesome-bio-agent-skills --skill species-trees --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: ASTER 1.15+ (ASTRAL-III/wASTRAL/ASTRAL-Pro), IQ-TREE 2.2+ (concordance factors), PAUP* 4.0a168+ (SVDQuartets) Before using code patterns, verify installed versions match. If versions differ: - CLI: `astral --version` then `astral --help` to confirm flags - CLI: `iqtree2 --version` then `iqtree2 --help` to confirm flags - CLI: PAUP* version displayed at startup If commands fail, introspect the installed version and adapt flags rather than retrying. # Coalescent-Based Species Tree Estimation **"Estimate a species tree from multi-locus data"** -> Infer the species-level phylogeny accounting for gene tree discordance caused by incomplete lineage sorting (ILS), using summary coalescent or full-likelihood methods. - CLI: `astral -i gene_trees.tre -o species_tree.tre` (ASTER/ASTRAL-III) - CLI: `iqtree2 -t species.tre --gcf gene_trees.tre -s concat.fasta --scfl 100` (concordance factors) - CLI: `svdquartets nquartets=all bootstrap=standard nreps=100` (PAUP*) ## When Concatenation Fails The multispecies coalescent (MSC) models gene tree discordance arising from incomplete lineage sorting. Concatenation assumes all genes share the same
- Version Compatibility
- When Concatenation Fails
- Concatenation vs Coalescent Decision
- Method Comparison
- ASTRAL Species Tree Pipeline
- Infer Gene Trees and Estimate Species Tree
- Compute Concordance Factors
- Interpreting Concordance Factors
- Interpretation Guide
- Distinguishing Quartet Asymmetry
- Gene Tree Estimation Error vs Biological Discordance
- SVDQuartets (Site-Pattern Method)
- BPP for Species Delimitation and Species Trees
- ASTRAL Branch Support and Branch Lengths
for f in loci/*.fasta; do
iqtree2 -s "$f" -m MFP -B 1000 -bnni -T 1 --prefix "${f%.fasta}"
done
cat loci/*.treefile > gene_trees.tre
Local posterior probability (pp) replaces bootstrap for branch support
astral -i gene_trees.tre -o species_tree.tre
wastral -i gene_trees.tre -o species_tree_wastral.tre
Gene concordance factors (gCF) + likelihood-based site concordance factors (sCF)
iqtree2 -t species_tree.tre --gcf gene_trees.tre -s concat.fasta --scfl 100
species_tree.tre.cf.stat (per-branch statistics)What does the bio-phylo-species-trees skill do?
Estimate species trees using coalescent methods including ASTRAL-III, wASTRAL, ASTRAL-Pro, SVDQuartets, and BPP. Use when multi-locus data shows gene tree discordance from incomplete lineage sorting, when in the anomaly zone where concatenation is misleading, or when computing concordance factors to assess topological support.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill species-trees --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.