With the increasing popularity of mitochondrial genome studies, the correct assembly and annotation of genomes are the basis

of all subsequent research into a species. Here we describe the protocols using Staden Package software to assemble and

annotate the mitochondrial genome, along with other commonly used software, such as ContigExpress, DNAMAN, DNASTAR, BioEdit

and Sequencher. In addition, methods for the use of different software packages (including DOGMA、MOSAS、MITOS、GOBASE、OGRe

、MitoZoa、tRNAscanSE、ARWEN、BLAST and MiTFi) to annotate mitochondrial genomic proteincoding genes, rRNA, tRNA and the

A+T region are briefly introduced. Finally, application of MEGA5 software to analyze the composition of mitochondrial

genomes, Sequin software to submit sequences to GenBank, and mitochondrial genome data visualization tools (CG view、MTviz

and OGDRAW) are also briefly introduced.