This is a site for the program ‘getmitogenome’ hosted in Kumazawa lab’s homepage. Questions and comments should be directed to Dr. Pierre Jonniaux ( 



by Pierre Jonniaux


   Getmitogenome is a script which mainly manipulates a complete or partial set of mitochondrial gene sequences from multiple taxa toward phylogenetic analyses. A complete set of gene sequences (amino acid sequences, as well) encoded in animal mitochondrial genomes can be retrieved from genbank or user’s personal data source (whether registered or unregistered to the public database). These gene sequences are automatically grouped, reordered and aligned against a pre-existing alignment for other taxa. Getmitogenome can also handle non-mitochondrial gene sequences based on user-assigned accession numbers to individual genes from multiple taxa. Please refer to the manual for more details.


   Getmitogenome is written in PERL, running on Mac and Linux OSes and distributed under the term of the GPL licence (meaning in short that it can be freely copied, modified and distributed as long as the original author is credited and the derived work is distributed under the same licence).

   If you can kindly cite my work, please use the following format:

Pierre Jonniaux. Getmitogenome: a software for manipulating animal mitochondrial gene sequences. accessed on **. ** should be the date when you downloaded the software.


   Script, Manual and Example_files for getmitogenome (


   This script was created during my Ph. D study course under the supervision by Prof. Yoshinori Kumazawa (Nagoya City University). I am greatly indebted to Drs. Takamasa Suzuki (Nagoya University) and Jun Inoue (University of Tokyo) for their invaluable inputs and supports to me and the software.

Your feedback should be directed to Pierre Jonniaux (

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Last Updated: November 21, 2012