PseudoChecker2 and PseudoViz: automation and visualization of gene loss in the Genome Era.

ABSTRACT:

Summary

High-fidelity genome assemblies provide unprecedented opportunities to decipher mechanisms of molecular evolution and phenotype landscapes. Here, we present PseudoChecker2, a command-line version of the web-tool PseudoChecker with expanded functions. It identifies gene loss via drastic mutational events such as premature stop codons, deletions and insertions. It enables the investigation of cross-species genomic datasets through: (i) integration into automated workflows, (ii) multiprocessing capability, and (iii) creation of a functional reference from annotation files. In addition, we introduce PseudoViz, a novel graphical interface designed to help interpret the results of PseudoChecker2 with intuitive visualizations. These tools combine the versatility and automation of

SUBMITTER: Resende-Pinto R 

PROVIDER: S-EPMC12679834 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature