Magma

Magma (Multiple Aligner of Genomic Multiple Alignments) is a fast, sensitive tool for whole regulome motif-finding in eukaryotic genomes (Ihuegbu, et al 2012).

We implemented this in C. elegans, using 5 other nematode genomes for conservation information, and present the discovered conserved, exemplar sites
( as UCSC bed tracks or a bed file ) and the motifs (as matrices and logos ).

You may download the Magma-1.0 source code here (patch modification: 04/27/2012).