The basic idea of this program is to align DNA sequencing fragments (shotgun or targeted resequencing) to a reference, then call a consensus. Then the consensus is used as new reference and the process is repeated until convergence. Since it was originally designed to be used on ancient DNA, it supports a position specific substitution matrix, which improves both alignment and consensus calling on chemically damaged aDNA.
MIA has been used to assemble a number of Neandertal and early modern human mitochondria. Occasionally it has been used on smallish nuclear regions, but it will probably not scale to a genome wide analysis.
This program takes the output of MIA and tries to make sure an assembled mitochondrion is free from contamination. It works by looking for positions in the called consensus where it differs from a panel of known human mitochondria, then classifies each read as either belonging to the sample or a putative contaminant.
If you get MIA from the Git repository, you will need the usual build environment (Gcc, Make, ...) and GNU Autotools (autoconf and automake). Installation should work like this:
sh bootstrap.sh ./configure make make install