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We present complete mitochondrial genomes (mitogenomes) for three orthopterans (Xyleus modestus, Physemacris variolosa, and Ellipes minuta) and describe MOSAS (manipulation, organization, storage, and analysis of sequences), software we developed to facilitate annotation and analysis. We analyze the base composition, start and stop codons, non-coding regions, and gene order among these and 18 other orthopteran mitogenomes from GenBank and reconstruct a phylogeny of Orthoptera. We propose a tetranucleotide start codon for cox1, and hypothesize that the tRNAAsp?tRNALys rearrangement is a synapomorphy for Acridomorpha, but not Caelifera. We further describe MOSAS, user-friendly software we used for this analysis. MOSAS streamlines sequence data storage, organization, annotation, and alignment, and provides convenient search tools for dataset construction and a robust annotation engine particularly suited to annotating mitogenomes (available at http://mosas.byu.edu).
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