The program libraries powering the core functions of MITOMASTER, CMEM Web's analytical component, are written in Perl and available from the comprehensive Perl archive network (CPAN):
Am finishing up the port of the alignment code as I write this for a first release of Bio::Mitomaster. This version will allow you to easily extract variants from a human mtDNA sequence, perform several types of sequence manipulation, including in silico transcription and translation, and provide easy access to ref sequence information. You might be interested in the project notes or email me if you have suggestions.
__ Marty Brandon