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JCVI MCScan

Status: available; repository minimum 1.6.5; current upstream 1.6.6 as of 2026-08-30.

JCVI provides Python MCScan workflows for pairwise and multi-species synteny. It can connect cluster-level findings to chromosome-scale conservation when suitable assemblies and annotations are available.

Install

python3 -m pip install "jcvi>=1.6.5"
python3 -m jcvi.compara.catalog --help

LAST or another documented alignment backend may also be required.

Output contract

Record source GFF and sequence identifiers, conversion commands, JCVI and backend versions, parameters, anchor files, plots, and hashes. Synteny claims should state assembly quality, annotation source, and any name normalization applied.

Sources: JCVI on PyPI and the MCScan guide.