bio-phylo-modern-tree-inference
Build maximum likelihood phylogenetic trees using IQ-TREE2 and RAxML-NG with expert model selection, branch support assessment, and topology testing. Use when inferring publication-quality ML trees, selecting substitution models, interpreting bootstrap and concordance factor support, or running partitioned phylogenomic analyses.
npx skills add BioTender-max/awesome-bio-agent-skills --skill modern-tree-inference --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: IQ-TREE 2.2+, RAxML-NG 1.2+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `iqtree2 --version` then `iqtree2 --help` to confirm flags - CLI: `raxml-ng --version` then `raxml-ng --help` to confirm flags If commands fail, introspect the installed version and adapt flags rather than retrying. # Modern ML Tree Inference **"Infer a maximum likelihood tree from my alignment"** -> Build publication-quality ML trees with automatic substitution model selection, ultrafast bootstrap support, concordance factors, and topology testing. - CLI: `iqtree2 -s alignment.fa -m MFP -B 1000 -alrt 1000 -bnni` (IQ-TREE2) - CLI: `raxml-ng --all --msa alignment.fa --model GTR+G --bs-trees 100` (RAxML-NG) ## IQ-TREE2 vs RAxML-NG Decision | Factor | IQ-TREE2 | RAxML-NG | |--------|----------|----------| | Model selection | Built-in ModelFinder | External ModelTest-NG | | Ultrafast bootstrap | UFBoot2 | No | | Branch lengths | Good | More accurate | | Concordance factors | Built-in (gCF/sCF) | No | | Very large trees (>1000 taxa) | Good | Better | | Transfer bootstrap | No | Yes | | Partition models | Extensive |
- Version Compatibility
- IQ-TREE2 vs RAxML-NG Decision
- Model Selection
- Use ModelFinder (-m MFP), Not -m TEST
- Rate Heterogeneity Models
- BIC vs AIC for Model Selection
- DNA Model Hierarchy
- Protein Models
- Branch Support Assessment
- Standard Analysis: UFBoot2 + SH-aLRT
- Interpreting Support Values
- When Low Support Matters
- Transfer Bootstrap (RAxML-NG)
- Concordance Factors
iqtree2 -s alignment.fasta -m MFP -B 1000 -alrt 1000 -bnni -T AUTO Model selection only (no tree inference) iqtree2 -s alignment.fasta -m MF -T AUTO Partition model with automatic merging iqtree2 -s concat.fasta -p partitions.nex -m MFP+MERGE -B 1000 -bnni -T AUTO Protein with ModelFinder iqtree2 -s protein.fasta -m MFP -B 1000 -bnni -st AA -T AUTO Protein with mixture model (for deep phylogenies) iqtree2 -s protein.fasta -m LG+C60+F+G -B 1000 -bnni -st AA -T AUTO Recommended for most analyses
What does the bio-phylo-modern-tree-inference skill do?
Build maximum likelihood phylogenetic trees using IQ-TREE2 and RAxML-NG with expert model selection, branch support assessment, and topology testing. Use when inferring publication-quality ML trees, selecting substitution models, interpreting bootstrap and concordance factor support, or running partitioned phylogenomic analyses.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill modern-tree-inference --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.