fasta-get-markov

Usage: fasta-get-markov <q> [options]

Description:

fasta-get-markov estimates a Markov model from a FASTA file of sequences. It Ignores (removes) ambiguous characters before computing the model. Both strands of DNA are combined unless -norc is set.

Input:

• Sequences in FASTA format from stdin

Output:

• Writes the Markov model in background model format to stdout.

Options:

• -m <n> - Order of Markov model to use. Default value is 0.
• -norc - Do not combine forward and reverse complement frequencies.
• -p - Use protein alphabet. Default is to use DNA alphabet.

Bugs: None known.

Author: Tim Bailey