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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, Institute of Science Tokyo
Lars Arvestad, Department of Mathematics, Stockholm University

Welcome!

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.

Installation

You are best off installing exonize from PyPI.org using

pip install exonize

If installing from the GitHub repo

git clone git@github.com: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

Requirements

exonize requires a local installation of: