Plant Breeding Python Packages

breedsim-mcp

MCP server for breeding-scheme simulation (AlphaSimR) — returns distributions, never a single stochastic run

ocs-rs

Exact, matrix-free, support-first solver for genomic optimum contribution selection (OCS), in Rust

pygapit-ng

Python implementation of GAPIT 3.5 for GWAS and genomic prediction, with disk-backed NumPy, HDF5, and Zarr workflows.

brapi-proxy

BrAPI proxy solution

progeny-selector

Ranks and selects progeny in marker-assisted backcross programs: foreground and avoid loci, recurrent-parent recovery, linkage-drag bounds, QC flags and a weighted composite score. Python core with a Shiny for Python UI.

dgnova

A Python library for Statistical Analysis and Simulations of Plant Breeding Experiments, designed specifically for researchers and students who are new to programming but want to understand field design concepts through practical implementation.

pynomic

Python library for data extraction from drone orthomosaics in plant breeding trials.

gsbench

The package is a CLI tool for benchmarking genomic selection models in plant breeding.