OrthoBrowser: gene family analysis and visualization.

Abstract

Motivation: The analysis of gene families across diverse species is pivotal in elucidating evolutionary dynamics and functional genomic landscapes. Typical analysis approaches often require significant computational expertise and user time.

Results: We introduce OrthoBrowser, a static site generator that will index and serve phylogeny, gene trees, multiple sequence alignments, and novel multiple synteny alignments. This greatly enhances the usability of tools like OrthoFinder by making the detailed results much more visually accessible. This interface can scale reasonably up to hundreds of genomes, allows a user to filter this large dataset to a subset of samples they are interested in at that particular moment in time, or "zoom in" to only a subtree of the orthogroup. The multiple synteny alignment method uses a progressive hierarchical alignment approach in the protein space using orthogroup membership to establish orthology. Orthobrowser makes it easy for users to identify, interact with, explore, and share key information about their gene families of interest.

Availability and implementation: OrthoBrowser is pip installable and is available under MIT license at: https://gitlab.com/salk-tm/orthobrowser. Complete example OrthoBrowser results are available at: https://orthobrowserexamples.netlify.app/.