EZmito2: a tool suite for mitochondrial genome dataset preparation, population genetics, and visualization

Abstract

Mitogenomic datasets are central to molecular evolution and phylogenetics, yet preparatory workflows remain labor-intensive and prone to errors introduced during manual data preparation. EZmito2 is a re-implementation of the widely used EZmito pipeline that offers a fully reproducible, and user-accessible solution for mitogenomic dataset curation and result visualization. It is accessible via a public web-server for rapid analyses and through local installation, enabling reproducible workflows on personal computers or computational clusters. The pipeline consolidates the core modules—EZpipe, EZskew, and EZcodon—and extends functionality through newly developed tools for genome visualization (EZcircular, EZmap), chimeric region detection (EZmix), gene extraction from NCBI-deposited genomes (EZsplit), structural annotation of transmembrane domains in mitochondrial protein-coding genes (EZtrampo) and for population genetic studies (EZdist, EZpcoa, EZpopstat). All tools accept standard input formats and generate ready-to-publish outputs. By providing a user-friendly platform for mitogenomic exploration and quality control, EZmito2 facilitates reproducible analyses for evolutionary and molecular research communities.