What's MaM?
MaM is a software tool that processes and manipulates multiple alignments of genomic sequences.

MaM computes the exact locations of common repeat elements in multiple aligned sequences, provided by a variety of user identified programs databases and tables.

It then graphically displays how the alignment quality varies throughout the aligned sequences, providing separate displays for the repeat and non-repeat portions.

Availability
MaM is freely available for non-commercial use. You can download it here. For more information, you can download the paper describing MaM here

Authors
The Authors of the program are Can Alkan and Eray Tuzun.