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USAGE:
meme <dataset> [optional arguments]
<dataset> file containing sequences in FASTA format
[-h] print this message
[-o <output dir>] name of directory for output files
will not replace existing directory
[-oc <output dir>] name of directory for output files
will replace existing directory
[-text] output in text format (default is HTML)
[-dna] sequences use DNA alphabet
[-protein] sequences use protein alphabet
[-mod oops|zoops|anr] distribution of motifs
[-nmotifs <nmotifs>] maximum number of motifs to find
[-evt <ev>] stop if motif E-value greater than <evt>
[-nsites <sites>] number of sites for each motif
[-minsites <minsites>] minimum number of sites for each motif
[-maxsites <maxsites>] maximum number of sites for each motif
[-wnsites <wnsites>] weight on expected number of sites
[-w <w>] motif width
[-minw <minw>] minimum motif width
[-maxw <maxw>] maximum motif width
[-nomatrim] do not adjust motif width using multiple
alignment
[-wg <wg>] gap opening cost for multiple alignments
[-ws <ws>] gap extension cost for multiple alignments
[-noendgaps] do not count end gaps in multiple alignments
[-bfile <bfile>] name of background Markov model file
[-revcomp] allow sites on + or - DNA strands
[-pal] force palindromes (requires -dna)
[-maxiter <maxiter>] maximum EM iterations to run
[-distance <distance>] EM convergence criterion
[-psp <pspfile>] name of positional priors file
[-prior dirichlet|dmix|mega|megap|addone]
type of prior to use
[-b <b>] strength of the prior
[-plib <plib>] name of Dirichlet prior file
[-spfuzz <spfuzz>] fuzziness of sequence to theta mapping
[-spmap uni|pam] starting point seq to theta mapping type
[-cons <cons>] consensus sequence to start EM from
[-heapsize <hs>] size of heaps for widths where substring
search occurs
[-x_branch] perform x-branching
[-w_branch] perform width branching
[-allw] include all motif widths from min to max
[-bfactor <bf>] branching factor for branching search
[-maxsize <maxsize>] maximum dataset size in characters
[-nostatus] do not print progress reports to terminal
[-p <np>] use parallel version with <np> processors
[-time <t>] quit before <t> CPU seconds consumed
[-sf <sf>] print <sf> as name of sequence file
[-V] verbose mode
[-version] display the version number and exit