Summary: Current approaches detect conserved genomic order either at chromosomal (macrosynteny) or at subchromosomal scales (microsynteny). The latter generally requires collinearity and hard thresholds on syntenic region size, thus excluding a major proportion of syntenies with recent expansions or minor rearrangements. 'SYNPHONI' bridges the gap between micro- and macrosynteny detection, providing detailed information on both synteny conservation and transformation throughout the evolutionary history of animal genomes.
Availability and implementation: Source code is freely available at https://github.com/nsmro/SYNPHONI, implemented in Python 3.9.
Supplementary information: Supplementary data are available at Bioinformatics online.
© The Author(s) 2022. Published by Oxford University Press.