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phylogenetics

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About phylogenetics

P

phylogenetics

Builds and analyzes phylogenetic trees

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.

View phylogeneticsAll AI Skills apps
Price
Free
Made by
k-dense-ai
Category
AI Skills
Website
github.com/k-dense-ai/scientific-agent-skills/phylogenetics