AI导哈

数据与研究

phylogenetics

k-dense-ai/scie…t-skills

Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein families, and cautiously interpreted dated phylogenies.

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安装命令

npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill phylogenetics

SKILL.md

Phylogenetics

When to use

Use this workflow for an alignment of homologous loci or proteins, a gene tree, branch support, and an interpretable tree figure. Multi-locus partitioning, concordance factors, ancestral states and dating are covered in IQ-TREE reference.

A gene tree does not establish a species tree, transmission direction, or horizontal transfer by itself. Sampling dates alone do not justify a molecular clock.

Versions and installation

Reviewed against current official documentation on 2026-10-01. The executed smoke workflow used MAFFT 7.526, IQ-TREE 3.1.4, FastTree 2.2.0 and ETE3 3.1.3 on Python 3.12. ETE3 remains deliberate for this helper; ETE4 is a separate API and is not a drop-in replacement. ETE3 imports cgi, removed in Python 3.13. The native executables are not Python packages.

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