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Inputs

Inputs. Tools. Results. Genbank files: tmp /< runname >/ gbks /*.gbk. alignAce parser. AlignAce. AnnSpec. annSpec parser. MTAPglobals.py. Elph. elph parser. Motifs: tmp /< runname >/ kmraws /*. blackfile *. redfile. Gibbs.

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Inputs

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  1. Inputs Tools Results Genbank files: tmp/<runname>/gbks/*.gbk alignAce parser AlignAce AnnSpec annSpec parser MTAPglobals.py Elph elph parser Motifs: tmp/<runname>/kmraws/*.blackfile *.redfile Gibbs Stats files: dumpdir/<runname>/<phylo>/<num_bases>/<cr/sr>/real/stats gibbs parser MTAPdbSetup.py Glam glam parser tmp/<runname>/accoc/accocs (genome name) MDscan mdscan parser Meme meme parser User Inputs (cr/sr, genic/phylo, number of bases, tools, center genome Mitra mitra parser PhyloGibbs phylogibbs parser Phyme phyme parser Tool selection Weeder weeder parser

  2. Inputs Tools Results Sequence to be analyzed alignAce parser AlignAce AnnSpec annSpec parser MTAPglobals.py Elph elph parser Motifs Gibbs Stats files: (number of true positives, true negatives, and false positives) gibbs parser MTAPdbSetup.py Glam glam parser Name of genome to be analyzed MDscan mdscan parser Meme meme parser User Inputs (genic/phylo, number of bases, tools) Mitra mitra parser PhyloGibbs phylogibbs parser Phyme phyme parser Tool selection Weeder weeder parser

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