evopython: a Python package for feature-focused, comparative genomic data exploration

Abstract

MotivationSoftware such as LiftOver allows for the intra- and inter-species conversion of genomic coordinates between genome assemblies, but this coordinate-centric workflow is naive to sequence alterations underling the conversion. For instance, it does not clarify the location of any insertions or deletions that might have occurred. ResultsTo facilitate inter-species, sequence-based analyses, we developed evopython, a simple, object-oriented Python package that enables the sequence-aware resolution of genomic coordinates directly from pairwise and multiple whole-genome alignment data. The output is a Python dictionary storing all information relevant to the alignment: the participating species names, the position of the alignment in each species genome assembly, and the aligned sequences. Availability and implementationThe source code and documentation are available at https://github.com/fiszbein-lab/evopython. Contactanafisz@bu.edu