etetoolkit
Category: life-sciences · License: GPL-3.0-or-later · Version: 2.1 · Includes scripts
Tags: phylogenetics, phylogenetic trees, Newick, evolutionary biology, bioinformatics
When to use it
Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Do not use it to infer trees from raw sequences; align sequences and infer a tree first.Example requests
Ask your agent in plain language, for example:- “How do I load a Newick file in ete4 and prune it down to just 12 taxa?”
- “I’m porting my lab’s old ete3 script to ete4 and it now fails with ‘NewickError’ on gene_tree.nwk, which has bootstrap support on internal nodes. The old code used Tree(‘gene_tree.nwk’, format=1) and
t & 'Hsap_1', then called node.is_leaf() and t.get_leaves(). Fix it and then label each internal node as duplication or speciation, where leaf names look like SPECIES_geneID.” - “I have two published trees for the same 40 bird species, one from mitochondrial genomes and one from nuclear loci. I want a number that tells me how different their branching patterns are, and I’d also like to know which splits they disagree on.”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.