Opentree Tools

Configuration File: opentree_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the opentree_tools.json configuration file.

Available Tools

OpenTree_get_induced_subtree (Type: OpenTreeTool)

Get a phylogenetic subtree (in Newick format) from the Open Tree of Life synthetic tree for a spe…

OpenTree_get_induced_subtree tool specification

Tool Information:

  • Name: OpenTree_get_induced_subtree

  • Type: OpenTreeTool

  • Description: Get a phylogenetic subtree (in Newick format) from the Open Tree of Life synthetic tree for a specified set of taxa. Returns the evolutionary tree connecting the given taxa, showing their branching relationships. Useful for constructing phylogenies for comparative studies. Example: OTT IDs 770315 (Homo sapiens), 417950 (Pan troglodytes), 158484 (Pan paniscus) returns the ape phylogeny showing Pan troglodytes and Pan paniscus as sister species.

Parameters:

  • ott_ids (string) (required) Comma-separated OTT IDs (at least 2). Examples: ‘770315,417950,158484’ (human, chimp, bonobo), ‘770315,417950,158484,770309’ (plus Homo genus).

Example Usage:

query = {
    "name": "OpenTree_get_induced_subtree",
    "arguments": {
        "ott_ids": "example_value"
    }
}
result = tu.run(query)

OpenTree_get_mrca (Type: OpenTreeTool)

Find the Most Recent Common Ancestor (MRCA) of a set of taxa in the Open Tree of Life synthetic p…

OpenTree_get_mrca tool specification

Tool Information:

  • Name: OpenTree_get_mrca

  • Type: OpenTreeTool

  • Description: Find the Most Recent Common Ancestor (MRCA) of a set of taxa in the Open Tree of Life synthetic phylogeny. Takes two or more OTT IDs and returns their MRCA with its taxonomic name and rank. Essential for understanding evolutionary relationships between species. Example: OTT IDs 770315 (Homo sapiens) and 417950 (Pan troglodytes) gives MRCA in subfamily Homininae.

Parameters:

  • ott_ids (string) (required) Comma-separated OTT IDs (at least 2). Use OpenTree_match_names to get IDs. Examples: ‘770315,417950’ (human + chimp), ‘770315,417950,158484’ (human + chimp + bonobo), ‘244265,417950’ (fruit fly + chimp).

Example Usage:

query = {
    "name": "OpenTree_get_mrca",
    "arguments": {
        "ott_ids": "example_value"
    }
}
result = tu.run(query)

OpenTree_get_taxon (Type: OpenTreeTool)

Get detailed taxonomy information for a taxon from the Open Tree of Life by its OTT ID. Returns t…

OpenTree_get_taxon tool specification

Tool Information:

  • Name: OpenTree_get_taxon

  • Type: OpenTreeTool

  • Description: Get detailed taxonomy information for a taxon from the Open Tree of Life by its OTT ID. Returns the taxon name, rank, synonyms, source databases (NCBI, GBIF, IRMNG), and flags indicating taxonomic status. Use OpenTree_match_names first to get OTT IDs from species names. Example: OTT ID 770315 returns Homo sapiens with rank ‘species’, synonyms, and NCBI/GBIF cross-references.

Parameters:

  • ott_id (integer) (required) Open Tree Taxonomy ID. Examples: 770315 (Homo sapiens), 417950 (Pan troglodytes), 158484 (Pan paniscus), 312031 (Homininae), 244265 (Drosophila melanogaster).

Example Usage:

query = {
    "name": "OpenTree_get_taxon",
    "arguments": {
        "ott_id": 10
    }
}
result = tu.run(query)

OpenTree_match_names (Type: OpenTreeTool)

Resolve species names to standardized Open Tree of Life taxonomy IDs (OTT IDs) using the TNRS (Ta…

OpenTree_match_names tool specification

Tool Information:

  • Name: OpenTree_match_names

  • Type: OpenTreeTool

  • Description: Resolve species names to standardized Open Tree of Life taxonomy IDs (OTT IDs) using the TNRS (Taxonomic Name Resolution Service). Takes one or more species names and finds matching taxa in the Open Tree taxonomy, which synthesizes NCBI, GBIF, IRMNG, and other taxonomic sources. Returns OTT IDs that can be used with other OpenTree tools to retrieve phylogenetic trees and evolutionary relationships. Example: ‘Homo sapiens’ resolves to OTT ID 770315.

Parameters:

  • names (string) (required) Comma-separated list of species or taxon names to resolve. Examples: ‘Homo sapiens’, ‘Homo sapiens,Pan troglodytes,Gorilla gorilla’, ‘Canis lupus,Felis catus’.

Example Usage:

query = {
    "name": "OpenTree_match_names",
    "arguments": {
        "names": "example_value"
    }
}
result = tu.run(query)