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.
(Optional) The name of a file of sequences in FASTA format. If omitted, the sequences are read from standard input.
Writes a Markov background model to standard output or optionally to a file.
|-m||n||Estimate a Markov model of order n.||A 0-order Markov model is estimated.|
|-full||Use exactly the of symbols in the sequences 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.|