MitoGeneExtractor

MitoGeneExtractor is a software to conveniently extract mitochondrial genes from next-generation sequencing libraries. 

MitoGeneExtractor aligns all given nucleotide sequences against a protein reference sequence to obtain a multiple sequence alignment. The recommended use case is to extract mitochondrial genes from sequencing libraries, e.g. from hybrid enrichment libraries sequenced on the Illumina platform. The individual alignments are computed by calling the Exonerate program, which must be installed.