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phylogenetics-builder

Infers maximum-likelihood phylogenetic trees from FASTA sequences via MSA, trimming, model selection, and IQ-TREE2 or RAxML-NG.

1.1k|257|Updated Feb 25, 2026
Search Tags:#phylogenetics#Bootstrap#msa#fasta#iqtree#maximum likelihood#raxml-ng
One-click install
npx skills add https://github.com/ClawBio/ClawBio --skill phylogenetics-builder
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: phylogenetics-builder
Source: https://github.com/ClawBio/ClawBio/tree/main/skills/phylogenetics-builder
Command: npx skills add https://github.com/ClawBio/ClawBio --skill phylogenetics-builder

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pandas, biopython, matplotlib, ete3.

What problem does it solve?

Building a maximum-likelihood phylogenetic tree requires correctly chaining at least five external tools (aligner, trimmer, model selector, tree engine, visualizer), each with conflicting CLI flags, incompatible model-name formats, and different bootstrap thresholds. This Skill automates the entire pipeline and handles tool quirks automatically.

Core Features & Use Cases

  • Full pipeline orchestration: Runs MSA (mafft, muscle, clustalw, kalign, tcoffee, prank), trimAl trimming, IQ-TREE2 ModelFinder model selection, and tree inference with IQ-TREE2 or RAxML-NG.
  • Flexible bootstrap and rooting: Supports UFBoot, standard Felsenstein, and triple support (UFBoot + aLRT + aBayes), plus outgroup or midpoint rooting.
  • Reproducible outputs: Generates a Markdown report, Newick tree, phylogram figure, branch support CSV, and a reproducibility bundle with exact commands, Conda environment, and SHA-256 checksums.
  • Use Case: A researcher has unaligned primate DNA sequences in a FASTA file and needs a publication-ready bootstrapped tree; the Skill aligns, trims, selects the best substitution model, infers the tree, and renders the figure in one command.

Quick Start

Ask the agent to build a maximum-likelihood phylogenetic tree from your sequences.fasta file using IQ-TREE2 with UFBoot support.

Frequently Asked Questions about phylogenetics-builder

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I build a maximum-likelihood phylogenetic tree from FASTA sequences?▼

Run the pipeline with your FASTA file and an output directory; it performs MSA with mafft, trims with trimAl, selects a model via IQ-TREE2 ModelFinder, and infers the tree with UFBoot support. Use --aligned if your sequences are already aligned to skip the MSA step.

IQ-TREE2 vs RAxML-NG for phylogenetic tree inference?▼

IQ-TREE2 is the default engine and includes built-in ModelFinder for automatic model selection. RAxML-NG is available via --engine raxml-ng, but note that ModelFinder's +F frequency token must be stripped from model names, which the Skill handles automatically.

What bootstrap threshold should I use with UFBoot?▼

UFBoot support values require a threshold of 95 or higher, not the 70 used for standard Felsenstein bootstrap. Applying the standard threshold to UFBoot values is a common mistake that overstates branch reliability.

Can I run phylogenetic tree inference without installing IQ-TREE or mafft?▼

Yes, in demo mode the Skill falls back to a precomputed 12-taxon primate tree when binaries are absent, so it always produces a result. For real data, install the tools via conda from the bioconda channel.

Why does RAxML-NG reject my substitution model string?▼

IQ-TREE ModelFinder appends +F (empirical frequencies) to model names like TIM3+F+G4, which RAxML-NG cannot parse. The Skill strips +F automatically via its model adaptation function; if passing --model manually with raxml-ng, omit +F yourself.

When should I skip trimAl trimming on my alignment?▼

Skip trimming with --no-trim for small protein alignments (under 20 sequences, over 200 amino acids), where trimAl's -automated1 strategy can remove too many informative columns. Trimming is most useful for removing gapped, noisy columns in larger alignments.

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