Hi! I'm looking for general purpose motif finder software, in the sense that I could input not aligned sequences and get a sequence logo or a PWM or the list of most frequent motifs I've found the cosmo r package
cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy.
But I have problems to find motifs using cosmo in sequences that don't have the 4 nucleotides, are you aware of motifs finders in that sort of sequences?