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hmm2emit - generate sequences from a profile HMM


hmm2emit [options] hmmfile


hmm2emit reads an HMM file from hmmfile containing one or more HMMs, and generates a
number of sequences from each HMM; or, if the -c option is selected, generate a single
majority-rule consensus. This can be useful for various applications in which one needs a
simulation of sequences consistent with a sequence family consensus.

By default, hmm2emit generates 10 sequences and outputs them in FASTA (unaligned) format.


-a Write the generated sequences in an aligned format (SELEX) rather than FASTA.

-c Predict a single majority-rule consensus sequence instead of sampling sequences
from the HMM's probability distribution. Highly conserved residues (p >= 0.9 for
DNA, p >= 0.5 for protein) are shown in upper case; others are shown in lower case.
Some insert states may become part of the majority rule consensus, because they are
used in >= 50% of generated sequences; when this happens, insert-generated residues
are simply shown as "x".

-h Print brief help; includes version number and summary of all options, including
expert options.

-n <n> Generate <n> sequences. Default is 10.

-o <f> Save the synthetic sequences to file <f> rather than writing them to stdout.

-q Quiet; suppress all output except for the sequences themselves. Useful for piping
or directing the output.


--seed <n>
Set the random seed to <n>, where <n> is a positive integer. The default is to use
time() to generate a different seed for each run, which means that two different
runs of hmm2emit on the same HMM will give slightly different results. You can use
this option to generate reproducible results.

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