EnsemblCompara Get Cafe Tree
Retrieve the Ensembl Compara CAFE tree for a gene family: the gene gain/loss (expansion/contraction) analysis that infers ancestral gene-copy counts (n_members) at every node of the species tree, with the birth-death rate (lambda) and per-node p-values. Unlike EnsemblCompara_get_gene_tree (which returns the phylogenetic gene tree topology + members), this returns the CAFE family-size dynamics used to detect lineage-specific gene-family expansions/contractions. Provide either gene_tree_id (e.g.…
Overview
Retrieve the Ensembl Compara CAFE tree for a gene family: the gene gain/loss (expansion/contraction) analysis that infers ancestral gene-copy counts (n_members) at every node of the species tree, with the birth-death rate (lambda) and per-node p-values. Unlike EnsemblCompara_get_gene_tree (which returns the phylogenetic gene tree topology + members), this returns the CAFE family-size dynamics used to detect lineage-specific gene-family expansions/contractions. Provide either gene_tree_id (e.g. 'ENSGT00390000003602') or gene (symbol e.g. 'BRCA2', or Ensembl gene ID). Example: gene_tree_id='ENSGT00390000003602' returns type 'cafe tree', rooted, pvalue_avg, lambda ~5.08e-08, and per-node n_members / pvalue along the species tree.
Schema
JSON Schema the agent (or your API call) must match.
View JSON schemaExpandCollapse
Examples (1)
Default EnsemblCompara Get Cafe Tree call
Public-safe example · rate-limited
Identifiers
- Catalog ID
- tu_EnsemblCompara_get_cafe_tree
- Tool name
- EnsemblCompara_get_cafe_tree
- Added
- 2026-07-29 18:13Z
- Tags
- tooluniverse