Agent skill · research science · k-dense-ai
phylogenetics
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
Why this skill is useful
Provides specific commands and workflows for phylogenetic analysis that the AI wouldn't reliably generate on its own.
What it needs
Requires ete3, fasttree, iqtree, mafft, pyqt5 installed locally. About 6k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
Phylogenetics Overview Phylogenetic analysis reconstructs the evolutionary history of biological sequences (genes, proteins, genomes) by inferring the branching pattern of descent. This skill covers the standard pipeline: 1. MAFFT — Multiple sequence alignment 2. IQ-TREE 2 — Maximum likelihood tree inference with model selection 3. FastTree — Fast approximate maximum likelihood (for large datasets) 4. ETE3 — Python library for tree manipulation and visualization Installation: When to Use This Skill Use phylogenetics when: Evolutionary relationships: Which organism/gene is most closely related to my sequence? Viral phylodynamics: Trace outbreak spread and estimate transmission dates Protein family analysis: Infer evolutionary relationships within a gene family Horizontal gene transfer detection: Identify genes with discordant species/gene trees Ancestral sequence reconstruction: Infer ancestral protein sequences Molecular clock analysis: Estimate divergence dates using temporal sampling GWAS companion: Place variants in evolutionary context (e.g., SARS-CoV-2 variants) Microbiology: Species phylogeny from 16S rRNA or core genome phylogeny Standard Workflow 1. Multiple Sequence Alignment with MAFFT 2. Trim Alignment (Optional but Recommended) 3. IQ-TREE 2 — Maximum Likelihood Tree 4. FastTree — Fast Approximate ML For large datasets (>1000 sequences) where IQ-TREE is too slow: 5. Tree Analysis and Visualization with ETE3 6. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/phylogenetics