Skip to content
Semidán Robaina Estévez edited this page Oct 4, 2022 · 6 revisions
Clone this wiki locally


Pynteny is a Python package to query sequence databases for synteny blocks through Hidden Markov Models (HMMs). It can be run in a command line interface or through a graphical interface. The command line tool is more complete and is intended to be employed in remote servers, whereas the graphical interface runs locally and may be easier to handle for some users (also intended for educational purposes).

These are the available subcommands, run as pynteny <subcommand> <options>:


There are two Jupyter notebooks with examples on how to use Pynteny's command-line interface as well as its Python API. Check them out here!


If you use this software, please cite it as below:

Semidán Robaina Estévez. (2022). Pynteny: synteny-aware hmm searches made easy(Version 0.0.2). Zenodo.