mhmme [options] <HMM filename>
Given a MEME Suite hidden Markov model (HMM), mhmme randomly generates sequence from the model and prints them in FASTA format.
An HMM in MEME Suite format must be provided. If the filename is given as '-', then mhmme will attempt to read the HMM from standard input.
The program prints to standard output one or more sequences in FASTA format.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| General Options | |||
| --numseq | count | The number of sequences to emit. | One sequence is generated. |
| --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 | seed | Set the seed for the random number generator. | The seed is set from the clock. |