MitoPhAST

MitoPhAST automates identification and alignment of mitochondrial protein-coding genes from GenBank/EMBL mitogenome files to produce concatenated, partitioned amino acid datasets for phylogenetic reconstruction.

Key Features:

• Automated identification and alignment: Identifies annotated protein-coding gene features in complete or partial mitogenome files (GenBank/EMBL) and generates standardized, concatenated, partitioned amino acid alignments.
• Phylogenetic tree generation: Constructs phylogenetic trees using maximum likelihood (ML) methods with optimized protein models and complements these reconstructions with Bayesian inference.
• Comprehensive data reporting: Produces sequence-level tables summarizing mitochondrial gene content to identify missing or duplicated genes and detect gene rearrangements.

Scientific Applications:

• Mitogenome-scale phylogenetics: Applied to analyses of 81 publicly available decapod mitogenomes plus eight newly sequenced Australian freshwater crayfish mitogenomes, including the first Gramastacus mitogenome, to test monophyly and relationships within Decapoda.
• Improved nodal support and taxonomic resolution: Produces phylogenetic trees with generally higher nodal support than fragment-based methods and can corroborate results from mtDNA fragments and nuclear markers while using full mitogenomic data.
• Mitogenome evolution and rearrangement discovery: Facilitated detection of novel mitochondrial DNA gene rearrangements in several Australian freshwater crayfish genera, supporting studies of elevated mitogenomic evolutionary change and rearrangement dynamics.

Methodology:

Identification of annotated protein-coding genes in GenBank/EMBL mitogenome files; generation of standardized, concatenated, partitioned amino acid alignments; phylogenetic reconstruction using maximum likelihood with optimized protein models and Bayesian inference; and output of sequence-level mitochondrial gene summary tables for detection of missing/duplicated genes and rearrangements.