MEME Suite



       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
       [-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