PHAST

MitoPhAST (PHAge Search Tool) is an automated tool that identifies annotated protein-coding gene features and generates a standardized, concatenated, and partitioned amino acid alignment directly from complete/partial GenBank/EMBL-format mitogenome flat files. Additionally, MitoPhAST generates a maximum likelihood phylogenetic tree using optimized protein models and reports various mitochondrial genes and sequence information in a table format.

MitoPhAST was tested with 81 publicly available decapod mitogenomes and eight new complete mitogenomes of Australian freshwater crayfishes, including the first for the genus Gramastacus. The recovered phylogenetic trees using both Bayesian and ML methods support the results of studies using fragments of mtDNA and nuclear markers and other smaller-scale studies using whole mitogenomes. Compared to the fragment-based phylogenies, nodal support values are generally higher despite reduced taxon sampling suggesting that utilizing more fully mitogenomic data is valuable.

The simple table output from MitoPhAST provides an efficient summary and statistical overview of the mitogenomes under study at the gene level, allowing the identification of missing or duplicated genes and gene rearrangements.