Fasta-get-markov estimates a Markov model from a FASTA file of sequences. It Ignores (removes) ambiguous characters before computing the model. Both strands of DNA are combined unless -norc is set.
Parent program: meme
MEME is a tool for discovering motifs in a group of related DNA or protein sequences. MEME takes as input a group of DNA or protein sequences and outputs as many motifs as requested up to a user-specified statistical confidence threshold. MEME uses statistical modeling techniques to automatically choose the best width, number of occurrences, and description for each motif.