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 strands when using a complementable alphabet 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. |
| -alph | alphabet file | Use the specified custom alphabet. | Autodetect DNA or protein alphabet. |
| -dna | Use DNA alphabet. | Autodetect DNA, protein or RNA alphabet. | |
| -protein | Use protein alphabet. | Autodetect DNA, protein or RNA alphabet. | |
| -rna | Use RNA alphabet. | Autodetect DNA, protein or RNA alphabet. | |
| -full | Use full list of seen symbols as the alphabet. | Autodetect DNA or protein alphabet. | |
| -counts | Output counts instead of probabilities and skip writing entries with no counts. Options -norc and -pseudo are ignored. | Output probabilities as normal. | |
| -norc | Do not combine forward and reverse complement frequencies for complementable alphabets. | ||
| -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. | |
| -nosummary | Do not display a summary report after completion even when a output background file is specified. | Display a summary report to standard output after the program has finished when a output background file has been specified. | |
| -help | Print a help message and exit. | Runs as normal. | |