get_gene_tree
Retrieve phylogenetic trees for gene families to analyze evolutionary relationships and gene function across species using Ensembl genomic data.
Instructions
Get phylogenetic tree for gene family
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| gene_id | Yes | Ensembl gene ID | |
| species | No | Species name (default: homo_sapiens) | |
| format | No | Tree format (default: json) | |
| clusterset_id | No | Specific clusterset ID (optional) |
Implementation Reference
- src/index.ts:1254-1288 (handler)The handler function for the 'get_gene_tree' tool. Validates input using isValidGeneTreeArgs, constructs Ensembl REST API request to /genetree/id/{gene_id}, handles format and clusterset_id parameters, fetches the phylogenetic tree data, and returns it as formatted text content.
private async handleGetGeneTree(args: any) { if (!isValidGeneTreeArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid gene tree arguments'); } try { const format = args.format || 'json'; let endpoint = `/genetree/id/${args.gene_id}`; const params: any = {}; if (args.clusterset_id) { params.clusterset_id = args.clusterset_id; } if (format !== 'json') { params.format = format; } const response = await this.apiClient.get(endpoint, { params }); return { content: [ { type: 'text', text: typeof response.data === 'object' ? JSON.stringify(response.data, null, 2) : String(response.data), }, ], }; } catch (error) { return this.handleError(error, 'fetching gene tree'); } } - src/index.ts:309-321 (schema)Input validation type guard (schema) for get_gene_tree tool arguments: requires gene_id string, optional species, format (json/newick/phyloxml), clusterset_id.
const isValidGeneTreeArgs = ( args: any ): args is { gene_id: string; species?: string; format?: string; clusterset_id?: string } => { return ( typeof args === 'object' && args !== null && typeof args.gene_id === 'string' && args.gene_id.length > 0 && (args.species === undefined || typeof args.species === 'string') && (args.format === undefined || ['json', 'newick', 'phyloxml'].includes(args.format)) && (args.clusterset_id === undefined || typeof args.clusterset_id === 'string') ); }; - src/index.ts:669-681 (registration)Tool registration definition in the listTools response, including name, description, and detailed inputSchema matching the validator.
name: 'get_gene_tree', description: 'Get phylogenetic tree for gene family', inputSchema: { type: 'object', properties: { gene_id: { type: 'string', description: 'Ensembl gene ID' }, species: { type: 'string', description: 'Species name (default: homo_sapiens)' }, format: { type: 'string', enum: ['json', 'newick', 'phyloxml'], description: 'Tree format (default: json)' }, clusterset_id: { type: 'string', description: 'Specific clusterset ID (optional)' }, }, required: ['gene_id'], }, }, - src/index.ts:851-852 (registration)Dispatch case in the CallToolRequestSchema switch statement that routes 'get_gene_tree' calls to the handleGetGeneTree handler.
case 'get_gene_tree': return this.handleGetGeneTree(args);