Sequence motif are parts of a sequence (most often referring to DNA) which are highly conserved across many sequences.

DTC project for using Gibbs sampling for DNA motif identification: folder (pdf)

http://meme-suite.org/

In this paper, we introduce a new type of motif-Ž nding problem, the Substring Parsimony Problem, which is a formalization of the phylogenetic footprinting idea, and which makes use of the phylogenetic tree underlying the data