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Ensembl Compara — comparative genomics database and API from EMBL-EBI providing pairwise and multiple whole-genome alignments, gene trees, protein families, orthologues, paralogues, and synteny region
Use with AI
Install the MCP server or CLI to instantly fetch Ensembl Compara documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/ensembl-compara
ASTRAL — fast species tree estimation from unrooted gene trees under the multi-species coalescent model. Handles incomplete lineage sorting (ILS) in phylogenomic datasets with hundreds of species and
3 shared topics • 2 shared operations
BEAST2 — Bayesian Evolutionary Analysis by Sampling Trees. Cross-platform Java application for Bayesian phylogenetic inference using MCMC sampling. Use when estimating time-calibrated phylogenies, rel
3 shared topics • 2 shared operations
OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se
3 shared topics • 2 shared operations
TreeTime — maximum likelihood molecular clock inference, ancestral sequence reconstruction, and phylodynamic analysis from time-stamped phylogenies. Infers timetrees by iteratively optimizing ancestra
3 shared topics • 2 shared operations
Ensembl REST API — HTTP/JSON web service for programmatic access to Ensembl genomic data without installing local databases. Supports gene/transcript/protein lookup by stable ID or gene symbol, sequen
2 shared topics • 3 shared operations