This web site,, contains data from the laboratory of Philipp W. Simon, USDA-ARS Vegetable Crops Research Unit [Click here for our web page]

Public MITOFY Analysis Web Server

The MITOFY home page is
If you publish an analysis using MITOFY, please cite the publication listed on the web site shown above. The algorithms of MITOFY have not been modified from the authors' version, however the versions of tRNAscan-SE and blast+ are different than the MacOS versions supplied in the original program.
This server uses the March 22, 2012 version of MITOFY, and is currently using version 1.3.1 of tRNAscan-SE, and version 2.11.0+ of the NCBI blast+ programs
This cgi program, and MITOFY files modified to allow use as a web-based cgi can be downloaded from
Contact information:

 Enter FASTA file for analysis by MITOFY:
or upload a file:
Project ID (required)
--prot_emax - maximum BLAST expect value for protein genes
--prot_pmin - minimum percent identity for protein genes
--rna_emax - maximum BLAST expect value for RNA genes
--rna_pmin - minimum percent identity for RNA genes
--rna_mlen - minimum length for RNA BLASTN matches