Pynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databases

Pynteny is Python tool to search for synteny blocks in (prokaryotic) sequence data through HMMs of the ORFs of interest and HMMER. By leveraging genomic context information, Pynteny can be employed to decrease the uncertainty of functional annotation of unlabelled sequence data due to the effect of paralogs. Pynteny can be accessed (i) through the command line, (ii) as a Python module or (iii) as a (locally served) web application.