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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)
        [-objfun classic|de|se|cd|ce]   objective function (default: classic)                                                                                                                                                                                                                                                                         [-test mhg|mbn|mrs]     statistical test type (default: mhg)
        [-use_llr]              use LLR in search for starts in Classic mode                                                                                                                                                                                                                                                                          [-neg <negdataset>]     file containing control sequences
        [-shuf <kmer>]          preserve frequencies of k-mers of size <kmer>                                                                                                                                                                                                                                                                                                 when shuffling (default: 2)
        [-hsfrac <hsfrac>]      fraction of primary sequences in holdout set                                                                                                                                                                                                                                                                                                  (default: 0.5)
        [-cefrac <cefrac>]      fraction sequence length for CE region                                                                                                                                                                                                                                                                                                        (default: 0.25)
        [-searchsize <ssize>]   maximum portion of primary dataset to use                                                                                                                                                                                                                                                                                                     for motif search (in characters)
        [-maxsize <maxsize>]    maximum dataset size in characters                                                                                                                                                                                                                                                                                    [-norand]               do not randomize the order of the input
                                sequences with -searchsize                                                                                                                                                                                                                                                                                            [-csites <csites>]      maximum number of sites for EM in Classic mode
        [-seed <seed>]          random seed for shuffling and sampling                                                                                                                                                                                                                                                                                [-dna]                  sequences use DNA alphabet
        [-rna]                  sequences use RNA alphabet                                                                                                                                                                                                                                                                                            [-protein]              sequences use protein alphabet
        [-alph <alph file>]     sequences use custom alphabet                                                                                                                                                                                                                                                                                         [-revcomp]              allow sites on + or - DNA strands
        [-pal]                  force palindromes (requires -dna)                                                                                                                                                                                                                                                                                     [-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>
        [-time <t>]             quit before <t> seconds have elapsed                                                                                                                                                                                                                                                                                  [-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
        [-allw]                 test starts of all widths from minw to maxw
        [-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
        [-markov_order <order>] (maximum) order of Markov model to use or create
        [-psp <pspfile>]        name of positional priors file
        [-maxiter <maxiter>]    maximum EM iterations to run
        [-distance <distance>]  EM convergence criterion
        [-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
        [-brief <n>]            omit sites and sequence tables in
                                output if more than <n> primary sequences
        [-nostatus]             do not print progress reports to terminal
        [-p <np>]               use parallel version with <np> processors
        [-sf <sf>]              print <sf> as name of sequence file
        [-V]                    verbose mode
        [-version]              display the version number and exit