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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