phylo-tree-workbench

Guides phylogenetic and hierarchical tree work with the ETE toolkit, structured around the decisions each request needs. Covers picking Tree, PhyloTree, ClusterTree or NCBITaxa, reading Newick and NHX with the correct format number, read-only questions such as distances, ancestry, monophyly and traversal, topology edits like rerooting, pruning and polytomy resolution gated on explicit confirmation, Robinson-Foulds comparison with partition differences, duplication and speciation calling with ortholog and paralog extraction, NCBI taxonomy lookup and species-tree building, silhouette and Dunn scoring of clustering dendrograms, and styled PDF, SVG and PNG rendering. Use when the user supplies gene trees, species trees, clustering dendrograms or taxon names and wants them inspected, edited, compared, annotated or drawn. Not for inferring trees from raw sequences, building multiple alignments, or general network analysis.

Version

v1.0.0

Size

19 KB

Updated

2026-10-10

Your client verifies the signature before reading. This explicit manual read is available on every plan. Free automatically loads five chosen skills; paid plans automatically load relevant skills across the library.