MCP Servers
MCP servers for plant genomics research with LLMs: locus lookup, dataset search, phenotyping, phylogenetics, breeding simulation, and a job broker.
Model Context Protocol servers I maintain, so an agent in Claude Code or another MCP client can look up a locus, find a dataset, measure a plant image, build a tree or simulate a breeding programme. Each is on PyPI and has a client config example in its README. Where a tool computes a number, it also returns what the number came from, such as the segmentation overlay, the bootstrap support or the spread across replicates.
- plant-genomics-mcp: 50+ tools across 23 public backends (Ensembl Plants, Phytozome, UniProt, AlphaFold DB, JASPAR, KEGG, STRING-DB and others). There is a hosted demo.
- data-aggregator-mcp: search and fetch datasets from Zenodo, DataCite, GEO/SRA, PubMed and OpenAIRE through one interface.
- plantcv-mcp: PlantCV trait measurements, returned with the segmentation overlay they were measured from. Batch mode applies a recipe you have checked that way.
- phylokit-mcp: phylogenetic inference with IQ-TREE 3 (through piqtree). Trees always come with bootstrap support.
- breedsim-mcp: breeding-scheme simulation with AlphaSimR. Reports mean, sd and CI across replicates rather than a single run. Needs R 4.3 or newer.
- jobd: a job broker for my own machines. It routes long jobs by GPU and tool tags and exposes the queue over MCP.
pip install plant-genomics-mcp data-aggregator-mcp plantcv-mcp phylokit-mcp breedsim-mcp jobd
Archived on Zenodo (concept DOIs): plant-genomics-mcp · data-aggregator-mcp · plantcv-mcp · phylokit-mcp · breedsim-mcp · jobd