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.


<sequence file>

(Optional) The name of a file of sequences in FASTA format. If omitted, the sequences are read from standard input.

[<background file>]

(Optional) The name of a file to receive the output. If omitted, writes to standard output. Must be omitted if reading from standard input.


Writes a Markov background model to standard output or optionally to a file.


Option Parameter Description Default Behavior
General Options
-mn 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.
-pseudocount 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.