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Mol Biol Evol. 2018 Jun 1;35(6):1553-1555. doi: 10.1093/molbev/msy074.

MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding.

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Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, Okinawa, Japan.
Department of Integrative Genomics, Tohoku Medial Megabank Organization, Tohoku University, Miyagi, Japan.
Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba, Chiba, Japan.
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.


Fish mitochondrial genome (mitogenome) data form a fundamental basis for revealing vertebrate evolution and hydrosphere ecology. Here, we report recent functional updates of MitoFish, which is a database of fish mitogenomes with a precise annotation pipeline MitoAnnotator. Most importantly, we describe implementation of MiFish pipeline for metabarcoding analysis of fish mitochondrial environmental DNA, which is a fast-emerging and powerful technology in fish studies. MitoFish, MitoAnnotator, and MiFish pipeline constitute a key platform for studies of fish evolution, ecology, and conservation, and are freely available at (last accessed April 7th, 2018).

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