Usage: mhmme [options] <HMM filename>
Description: Given a MEME Suite hidden Markov model (HMM), mhmme randomly generates sequence from the model and prints them in FASTA format.
Input: <HMM file> – An HMM in Meta-MEME format must be provided. If the filename is given as ‘-‘, then ‘mhmme’ will attempt to read the HMM from standard input.
Output: The mhmme program prints to standard output one or more sequences in Fasta format.
Options:
| Option | Description and default behavior |
| –occurs | Rather than printing the raw sequence, print a pseudo-sequence in which non-motif regions are represented as hyphens and motifs are represented like this: *____7___*, where 7 is the motif index. The output is normal FASTA format. |
| –seed | Set the seed for the random number generator. The seed is set from the clock. |
| –numseq | The number of sequences to emit. One sequence is generated. |