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 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.
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