Published June 19, 2026 | Version v1.3.0
Software Open

Pynteny: synteny-aware hmm searches made easy

Authors/Creators

  • 1. Department of Microbiology. University of La Laguna. Spain

Description

Pynteny 1.3.0

New

  • --best_hmm_wins option for synteny search (pynteny search --best_hmm_wins, or best_hmm_wins=True via the Python API). When the same peptide is hit by more than one HMM (paralog cross-hits), only the highest-scoring HMM for that peptide is kept before matching the synteny structure. This fixes cases where paralog cross-hits caused genuine syntenic blocks to be dropped (#96, via #103). Opt-in and default off, so existing behaviour is unchanged.

Full changelog: https://github.com/Robaina/Pynteny/compare/v1.2.0...v1.3.0

Notes

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

Files

Robaina/Pynteny-v1.3.0.zip

Files (2.7 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/Robaina/Pynteny/tree/v1.3.0 (URL)

Software

Repository URL
https://github.com/Robaina/Pynteny