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Marina Herrera Sarrias, Department of Mathematics, Stockholm University
Christopher Wheat, Department of Zoology, Stockholm University
Liam M. Longo, Earth-Life Science Institute (ELSI), Institute of Science Tokyo
Lars Arvestad, Department of Mathematics, Stockholm University
exonize is an open-source command-line tool and Python package for identifying and classifying coding exon duplications in annotated genomes. exonize identifies full exon duplications using local and global alignment methods and implements a graph-based framework to handle clusters of exons formed by repetitive duplication events. exonize introduces a classification schema to categorize the interdependence between duplicated exons (or groups of exons) across transcripts. For data parsing and downstream analysis, we introduce exonize_analysis a Python module within the exonize package.
Please see the Documentation for a full user guide and an introductory tutorial to the exonize_analysis module.
You are best off installing exonize from PyPI.org using
pip install exonizeIf installing from the GitHub repo
git clone [email protected]:msarrias/exonize.git
cd exonize
pip install .You should now be able to run exonize -h.
exonize is tested with Python 3.9, 3.10, 3.11, 3.12
exonize requires a local installation of:
If you need help with exonize, contact us! To report a bug or request a new feature, open an Issue on the exonize repo.
If you use exonize in a publication, please cite:
TBA