Description
phylogenetics is an agent skill for building and analysing phylogenetic trees from alignments of homologous DNA or protein sequences. It covers the gene tree, branch support, and an interpretable tree figure. The workflow uses MAFFT for multiple sequence alignment, IQ-TREE for maximum likelihood trees with ModelFinder and branch support, and FastTree for fast tree inference. Multi-locus partitioning, concordance factors, ancestral states and dating are covered in a separate IQ-TREE reference. The skill is clear about what a tree can show. A gene tree does not establish a species tree, the direction of transmission, or horizontal gene transfer on its own, and sampling dates alone do not justify a molecular clock. The versions were reviewed against current official documentation on 1 October 2026. 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. The skill keeps ETE3 for its helper, because ETE4 is a separate API and not a drop-in replacement. ETE3 imports cgi, which Python 3.13 removed. The native executables are not Python packages, so they must be installed separately.…
Highlights
- MAFFT alignment and IQ-TREE maximum likelihood
- ModelFinder and branch support
- FastTree for fast inference
- Tree figures
- Clear limits on what a gene tree shows
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phylogenetics FAQ
What does the workflow produce?
A phylogenetic tree from an alignment of homologous sequences, with branch support and a tree figure.
Which tools does it use?
MAFFT for alignment, IQ-TREE for maximum likelihood with ModelFinder, and FastTree for fast inference.
Can a gene tree show a species tree?
Not by itself. The skill says a gene tree does not establish a species tree, transmission direction or horizontal transfer.
Which versions were run?
MAFFT 7.526, IQ-TREE 3.1.4, FastTree 2.2.0 and ETE3 3.1.3 on Python 3.12.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill phylogenetics.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best phylogenetics alternatives?
Popular alternatives to phylogenetics include etetoolkit, gget and adaptyv. See all phylogenetics alternatives