fasta-get-markov [options] [sequence file] [background file]
The program fasta-get-markov estimates a Markov model from a FASTA file of sequences. It ignores (removes) ambiguous characters before computing the model. The model is based on both DNA strands unless you specify -norc.
Sequences in FASTA format from standard input or optionally specified as a file.
Writes a Markov background model to standard output or optionally to a file.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| General Options | |||
| -m | n | Use a Markov model of n-order. | A 0-order Markov model is used. |
| -norc | Do not combine forward and reverse complement frequencies. | ||
| -p | Use protein alphabet. | Use DNA alphabet. | |
| -pseudo | count | Pseudocount added to avoid probabilities of zero. | Adds a pseudocount of 0.1. |
| -nostatus | Do not display progress messages to standard error. | Displays a progress message every half a second. | |
| -help | Print a help message and exit. | Runs as normal. | |