title: MEME tags: [maunal, tools] date: 7/27/2016 6:40:19 PM

GCModeller [version 1.34.0.2]

Module AssemblyName: file:///G:/GCModeller/manual/bin/MEME.exe Root namespace: MEME.CLI

All of the command that available in this program has been list below:

Function API	Info
/BBH.Select.Regulators	Select bbh result for the regulators in RegPrecise database from the regulon bbh data.
/Build.FamilyDb
/Copys
/Copys.DIR
/CORN
/EXPORT.MotifDraws
/Export.MotifSites	Motif iteration step 1
/Export.Regprecise.Motifs
/Export.Similarity.Hits	Motif iteration step 2
/Footprints	3 - Generates the regulation footprints.
/Hits.Context	2
/LDM.Compares
/LDM.MaxW
/LDM.Selects
/MAST.MotifMatches
/MAST.MotifMatchs.Family	1
/mast.Regulations
/MAST_LDM.Build
/MEME.Batch	Batch meme task by using tmod toolbox.
/MEME.LDMs
/Motif.BuildRegulons
/Motif.Info	Assign the phenotype information And genomic context Info for the motif sites. [SimpleSegment] -> [MotifLog]
/Motif.Info.Batch	[SimpleSegment] -> [MotifLog]
/Motif.Similarity	Export of the calculation result from the tomtom program.
/MotifHits.Regulation
/Parser.DEGs
/Parser.Locus
/Parser.Log2
/Parser.MAST
/Parser.Modules
/Parser.Operon
/Parser.Pathway
/Parser.RegPrecise.Operons
/Parser.Regulon
/Parser.Regulon.gb
/Parser.Regulon.Merged
/Regulator.Motifs
/Regulator.Motifs.Test
/regulon.export
/Regulon.Reconstruct
/Regulon.Reconstruct2
/Regulon.Reconstructs	Doing the regulon reconstruction job in batch mode.
/Regulon.Test
/RfamSites
/seq.logo
/Similarity.Union	Motif iteration step 3
/Site.MAST_Scan	[MAST.Xml] -> [SimpleSegment]
/Site.MAST_Scan.Batch	[MAST.Xml] -> [SimpleSegment]
/Site.RegexScan
/site.scan
/SiteHits.Footprints	Generates the regulation information.
/SWTOM.Compares
/SWTOM.Compares.Batch
/SWTOM.LDM
/SWTOM.Query
/SWTOM.Query.Batch
/Tom.Query
/Tom.Query.Batch
/TomTOM
/TomTom.LDM
/TomTOM.Similarity
/TOMTOM.Similarity.Batch
/TomTom.Sites.Groups
/Trim.MastSite
--build.Regulations	Genome wide step 2
--build.Regulations.From.Motifs
--CExpr.WGCNA
Download.Regprecise	Download Regprecise database from Web API
--Dump.KEGG.Family
--family.statics
--Get.Intergenic
--GetFasta
--hits.diff
--Intersect.Max
--logo.Batch
--mapped-Back
mast.compile
mast.compile.bulk	Genome wide step 1
--modules.regulates	Exports the Venn diagram model for the module regulations.
Motif.Locates
MotifScan	Scan for the motif site by using fragment similarity.
--pathway.regulates	Associates of the pathway regulation information for the predicted virtual footprint information.
Regprecise.Compile	The repository parameter is a directory path which is the regprecise database root directory in the GCModeller directory, if you didn't know how to set this value, please leave it blank.
regulators.bbh	Compiles for the regulators in the bacterial genome mapped on the regprecise database using bbh method.
regulators.compile	Regprecise regulators data source compiler.
--site.Match
--site.Matches
--site.Matches.text	Using this function for processing the meme text output from the tmod toolbox.
--site.stat	Statics of the PCC correlation distribution of the regulation
--TCS.Module.Regulations
--TCS.Regulations
VirtualFootprint.DIP	Associate the dip information with the Sigma 70 virtual footprints.
wGet.Regprecise	Download Regprecise database from REST API

Commands

Help for command '/BBH.Select.Regulators':

Prototype: MEME.CLI::Int32 SelectRegulatorsBBH(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Select bbh result for the regulators in RegPrecise database from the regulon bbh data.
  Usage:        G:\GCModeller\manual\bin\MEME.exe /BBH.Select.Regulators /in <bbh.csv> /db <regprecise_downloads.DIR> [/out <out.csv>]
  Example:      MEME /BBH.Select.Regulators

Help for command '/Build.FamilyDb':

Prototype: MEME.CLI::Int32 BuildFamilyDb(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Build.FamilyDb /prot <RegPrecise.prot.fasta> /pfam <pfam-string.csv> [/out <out.Xml>]
  Example:      MEME /Build.FamilyDb

Help for command '/Copys':

Prototype: MEME.CLI::Int32 BatchCopy(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Copys /in <inDIR> [/out <outDIR> /file <meme.txt>]
  Example:      MEME /Copys

Help for command '/Copys.DIR':

Prototype: MEME.CLI::Int32 BatchCopyDIR(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Copys.DIR /in <inDIR> /out <outDIR>
  Example:      MEME /Copys.DIR

Help for command '/CORN':

Prototype: MEME.CLI::Int32 CORN(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /CORN /in <operons.csv> /mast <mastDIR> /PTT <genome.ptt> [/out <out.csv>]
  Example:      MEME /CORN

Help for command '/EXPORT.MotifDraws':

Prototype: MEME.CLI::Int32 ExportMotifDraw(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /EXPORT.MotifDraws /in <virtualFootprints.csv> /MEME <meme.txt.DIR> /KEGG <KEGG_Modules/Pathways.DIR> [/pathway /out <outDIR>]
  Example:      MEME /EXPORT.MotifDraws

Help for command '/Export.MotifSites':

Prototype: MEME.CLI::Int32 ExportTestMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Motif iteration step 1
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Export.MotifSites /in <meme.txt> [/out <outDIR> /batch]
  Example:      MEME /Export.MotifSites

Help for command '/Export.Regprecise.Motifs':

Prototype: MEME.CLI::Int32 ExportRegpreciseMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe 
  Example:      MEME /Export.Regprecise.Motifs

Help for command '/Export.Similarity.Hits':

Prototype: MEME.CLI::Int32 LoadSimilarityHits(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Motif iteration step 2
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Export.Similarity.Hits /in <inDIR> [/out <out.Csv>]
  Example:      MEME /Export.Similarity.Hits

Help for command '/Footprints':

Prototype: MEME.CLI::Int32 ToFootprints(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  3 - Generates the regulation footprints.
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Footprints /footprints <footprints.xml> /coor <name/DIR> /DOOR <genome.opr> /maps <bbhMappings.Csv> [/out <out.csv> /cuts <0.65> /extract]
  Example:      MEME /Footprints

Parameters information:

       [/extract]
    Description:  Extract the DOOR operon when the regulated gene is the first gene of the operon.

    Example:      /extract ""

Accepted Types

/extract

Help for command '/Hits.Context':

Prototype: MEME.CLI::Int32 HitContext(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  2
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Hits.Context /footprints <footprints.Xml> /PTT <genome.PTT> [/out <out.Xml> /RegPrecise <RegPrecise.Regulations.Xml>]
  Example:      MEME /Hits.Context

Help for command '/LDM.Compares':

Prototype: MEME.CLI::Int32 CompareMotif(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /LDM.Compares /query <query.LDM.Xml> /sub <subject.LDM.Xml> [/out <outDIR>]
  Example:      MEME /LDM.Compares

Help for command '/LDM.MaxW':

Prototype: MEME.CLI::Int32 LDMMaxLen(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /LDM.MaxW [/in <sourceDIR>]
  Example:      MEME /LDM.MaxW

Help for command '/LDM.Selects':

Prototype: MEME.CLI::Int32 Selectes(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /LDM.Selects /trace <footprints.xml> /meme <memeDIR> [/out <outDIR> /named]
  Example:      MEME /LDM.Selects

Help for command '/MAST.MotifMatches':

Prototype: MEME.CLI::Int32 MotifMatch2(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /MAST.MotifMatches /meme <meme.txt.DIR> /mast <MAST_OUT.DIR> [/out <out.csv>]
  Example:      MEME /MAST.MotifMatches

Help for command '/MAST.MotifMatchs.Family':

Prototype: MEME.CLI::Int32 MotifMatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  1
  Usage:        G:\GCModeller\manual\bin\MEME.exe /MAST.MotifMatchs.Family /meme <meme.txt.DIR> /mast <MAST_OUT.DIR> [/out <out.Xml>]
  Example:      MEME /MAST.MotifMatchs.Family

Help for command '/mast.Regulations':

Prototype: MEME.CLI::Int32 MastRegulations(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /mast.Regulations /in <mastSites.Csv> /correlation <sp_name/DIR> /DOOR <DOOR.opr> [/out <footprint.csv> /cut <0.65>]
  Example:      MEME /mast.Regulations

Help for command '/MAST_LDM.Build':

Prototype: MEME.CLI::Int32 BuildPWMDb(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /MAST_LDM.Build /source <sourceDIR> [/out <exportDIR:=./> /evalue <1e-3>]
  Example:      MEME /MAST_LDM.Build

Help for command '/MEME.Batch':

Prototype: MEME.CLI::Int32 MEMEBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Batch meme task by using tmod toolbox.
  Usage:        G:\GCModeller\manual\bin\MEME.exe /MEME.Batch /in <inDIR> [/out <outDIR> /evalue <1> /nmotifs <30> /mod <zoops> /maxw <100>]
  Example:      MEME /MEME.Batch

Parameters information:

    /in
    Description:  A directory path which contains the fasta sequence for the meme motifs analysis.

    Example:      /in ""

   [/out]
    Description:  A directory path which outputs the meme.txt data to that directory.

    Example:      /out ""

Accepted Types

/in

/out

Help for command '/MEME.LDMs':

Prototype: MEME.CLI::Int32 MEME2LDM(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /MEME.LDMs /in <meme.txt> [/out <outDIR>]
  Example:      MEME /MEME.LDMs

Help for command '/Motif.BuildRegulons':

Prototype: MEME.CLI::Int32 BuildRegulons(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Motif.BuildRegulons /meme <meme.txt.DIR> /model <FootprintTrace.xml> /DOOR <DOOR.opr> /maps <bbhmappings.csv> /corrs <name/DIR> [/cut <0.65> /out <outDIR>]
  Example:      MEME /Motif.BuildRegulons

Help for command '/Motif.Info':

Prototype: MEME.CLI::Int32 MotifInfo(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Assign the phenotype information And genomic context Info for the motif sites. [SimpleSegment] -> [MotifLog]
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Motif.Info /loci <loci.csv> [/motifs <motifs.DIR> /gff <genome.gff> /atg-dist 250 /out <out.csv>]
  Example:      MEME /Motif.Info

Parameters information:

    /loci
    Description:  The motif site info data set, type Is simple segment.

    Example:      /loci ""

/motifs
    Description:  A directory which contains the motifsitelog data in the xml file format. Regulogs.Xml source directory

    Example:      /motifs ""

Accepted Types

/loci

/motifs

Help for command '/Motif.Info.Batch':

Prototype: MEME.CLI::Int32 MotifInfoBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  [SimpleSegment] -> [MotifLog]
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Motif.Info.Batch /in <sites.csv.inDIR> /gffs <gff.DIR> [/motifs <regulogs.motiflogs.MEME.DIR> /num_threads -1 /atg-dist 350 /out <out.DIR>]
  Example:      MEME /Motif.Info.Batch

Parameters information:

    /motifs
    Description:  Regulogs.Xml source directory

    Example:      /motifs ""

   [/num_threads]
    Description:  Default Is -1, means auto config of the threads number.

    Example:      /num_threads ""

Accepted Types

/motifs

/num_threads

Help for command '/Motif.Similarity':

Prototype: MEME.CLI::Int32 MEMETOM_MotifSimilarity(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Export of the calculation result from the tomtom program.
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Motif.Similarity /in <tomtom.DIR> /motifs <MEME_OUT.DIR> [/out <out.csv> /bp.var]
  Example:      MEME /Motif.Similarity

Help for command '/MotifHits.Regulation':

Prototype: MEME.CLI::Int32 HitsRegulation(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /MotifHits.Regulation /hits <motifHits.Csv> /source <meme.txt.DIR> /PTT <genome.PTT> /correlates <sp/DIR> /bbh <bbhh.csv> [/out <out.footprints.Csv>]
  Example:      MEME /MotifHits.Regulation

Help for command '/Parser.DEGs':

Prototype: MEME.CLI::Int32 ParserDEGs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Parser.DEGs /degs <deseq2.csv> /PTT <genomePTT.DIR> /door <genome.opr> /out <out.DIR> [/log-fold 2]
  Example:      MEME /Parser.DEGs

Help for command '/Parser.Locus':

Prototype: MEME.CLI::Int32 ParserLocus(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Parser.Locus /locus <locus.txt> /PTT <genomePTT.DIR> /DOOR <genome.opr> [/out <out.DIR>]
  Example:      MEME /Parser.Locus

Help for command '/Parser.Log2':

Prototype: MEME.CLI::Int32 ParserLog2(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Parser.Log2 /in <log2.csv> /PTT <genomePTT.DIR> /DOOR <genome.opr> [/factor 1 /out <outDIR>]
  Example:      MEME /Parser.Log2

Help for command '/Parser.MAST':

Prototype: MEME.CLI::Int32 ParserMAST(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Parser.MAST /sites <mastsites.csv> /ptt <genome-context.pttDIR> /door <genome.opr> [/out <outDIR>]
  Example:      MEME /Parser.MAST

Help for command '/Parser.Modules':

Prototype: MEME.CLI::Int32 ModuleParser(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Parser.Modules /KEGG.Modules <KEGG.modules.DIR> /PTT <genomePTT.DIR> /DOOR <genome.opr> [/locus <union/initx/locus, default:=union> /out <fasta.outDIR>]
  Example:      MEME /Parser.Modules

Help for command '/Parser.Operon':

Prototype: MEME.CLI::Int32 ParserNextIterator(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Parser.Operon /in <footprint.csv> /PTT <PTTDIR> [/out <outDIR> /family /offset <50> /all]
  Example:      MEME /Parser.Operon

Parameters information:

       [/family]
    Description:  Group the source by family? Or output the source in one fasta set

    Example:      /family ""

Accepted Types

/family

Help for command '/Parser.Pathway':

Prototype: MEME.CLI::Int32 PathwayParser(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Parser.Pathway /KEGG.Pathways <KEGG.pathways.DIR> /PTT <genomePTT.DIR> /DOOR <genome.opr> [/locus <union/initx/locus, default:=union> /out <fasta.outDIR>]
  Example:      MEME /Parser.Pathway

Help for command '/Parser.RegPrecise.Operons':

Prototype: MEME.CLI::Int32 ParserRegPreciseOperon(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Parser.RegPrecise.Operons /operon <operons.Csv> /PTT <PTT_DIR> [/corn /DOOR <genome.opr> /id <null> /locus <union/initx/locus, default:=union> /out <outDIR>]
  Example:      MEME /Parser.RegPrecise.Operons

Help for command '/Parser.Regulon':

Prototype: MEME.CLI::Int32 RegulonParser(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Parser.Regulon /inDIR <regulons.inDIR> /out <fasta.outDIR> /PTT <genomePTT.DIR> [/door <genome.opr>]
  Example:      MEME /Parser.Regulon

Help for command '/Parser.Regulon.gb':

Prototype: MEME.CLI::Int32 RegulonParser2(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Parser.Regulon.gb /inDIR <regulons.inDIR> /out <fasta.outDIR> /gb <genbank.gbk> [/door <genome.opr>]
  Example:      MEME /Parser.Regulon.gb

Help for command '/Parser.Regulon.Merged':

Prototype: MEME.CLI::Int32 RegulonParser3(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Parser.Regulon.Merged /in <merged.Csv> /out <fasta.outDIR> /PTT <genomePTT.DIR> [/DOOR <genome.opr>]
  Example:      MEME /Parser.Regulon.Merged

Help for command '/Regulator.Motifs':

Prototype: MEME.CLI::Int32 RegulatorMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Regulator.Motifs /bbh <bbh.csv> /regprecise <genome.DIR> [/out <outDIR>]
  Example:      MEME /Regulator.Motifs

Help for command '/Regulator.Motifs.Test':

Prototype: MEME.CLI::Int32 TestRegulatorMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Regulator.Motifs.Test /hits <familyHits.Csv> /motifs <motifHits.Csv> [/out <out.csv>]
  Example:      MEME /Regulator.Motifs.Test

Help for command '/regulon.export':

Prototype: MEME.CLI::Int32 ExportRegulon(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /regulon.export /in <sw-tom_out.DIR> /ref <regulon.bbh.xml.DIR> [/out <out.csv>]
  Example:      MEME /regulon.export

Help for command '/Regulon.Reconstruct':

Prototype: MEME.CLI::Int32 RegulonReconstruct(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Regulon.Reconstruct /bbh <bbh.csv> /genome <RegPrecise.genome.xml> /door <operon.door> [/out <outfile.csv>]
  Example:      MEME /Regulon.Reconstruct

Help for command '/Regulon.Reconstruct2':

Prototype: MEME.CLI::Int32 RegulonReconstructs2(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Regulon.Reconstruct2 /bbh <bbh.csv> /genome <RegPrecise.genome.DIR> /door <operons.opr> [/out <outDIR>]
  Example:      MEME /Regulon.Reconstruct2

Help for command '/Regulon.Reconstructs':

Prototype: MEME.CLI::Int32 RegulonReconstructs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Doing the regulon reconstruction job in batch mode.
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Regulon.Reconstructs /bbh <bbh_EXPORT_csv.DIR> /genome <RegPrecise.genome.DIR> [/door <operon.door> /out <outDIR>]
  Example:      MEME /Regulon.Reconstructs

Parameters information:

    /bbh
    Description:  A directory which contains the bbh export csv data from the localblast tool.

    Example:      /bbh ""

/genome
    Description:  The directory which contains the RegPrecise bacterial genome downloads data from the RegPrecise web server.

    Example:      /genome ""

/door
    Description:  Door file which is the prediction data of the bacterial operon.

    Example:      /door ""

Accepted Types

/bbh

/genome

/door

Help for command '/Regulon.Test':

Prototype: MEME.CLI::Int32 RegulonTest(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Regulon.Test /in <meme.txt> /reg <genome.bbh.regulon.xml> /bbh <maps.bbh.Csv>
  Example:      MEME /Regulon.Test

Help for command '/RfamSites':

Prototype: MEME.CLI::Int32 RfamSites(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /RfamSites /source <sourceDIR> [/out <out.fastaDIR>]
  Example:      MEME /RfamSites

Help for command '/seq.logo':

Prototype: MEME.CLI::Int32 SequenceLogoTask(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /seq.logo /in <meme.txt> [/out <outDIR>]
  Example:      MEME /seq.logo

Help for command '/Similarity.Union':

Prototype: MEME.CLI::Int32 UnionSimilarity(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Motif iteration step 3
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Similarity.Union /in <preSource.fasta.DIR> /meme <meme.txt.DIR> /hits <similarity_hist.Csv> [/out <out.DIR>]
  Example:      MEME /Similarity.Union

Help for command '/Site.MAST_Scan':

Prototype: MEME.CLI::Int32 SiteMASTScan(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  [MAST.Xml] -> [SimpleSegment]
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Site.MAST_Scan /mast <mast.xml/DIR> [/batch /out <out.csv>]
  Example:      MEME /Site.MAST_Scan

Parameters information:

       [/batch]
    Description:  If this parameter presented in the CLI, then the parameter /mast will be used as a DIR.

    Example:      /batch ""

Accepted Types

/batch

Help for command '/Site.MAST_Scan.Batch':

Prototype: MEME.CLI::Int32 SiteMASTScanBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  [MAST.Xml] -> [SimpleSegment]
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Site.MAST_Scan /mast <mast.xml.DIR> [/out <out.csv.DIR> /num_threads <-1>]
  Example:      MEME /Site.MAST_Scan.Batch

Help for command '/Site.RegexScan':

Prototype: MEME.CLI::Int32 SiteRegexScan(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Site.RegexScan /meme <meme.txt> /nt <nt.fasta> [/batch /out <out.csv>]
  Example:      MEME /Site.RegexScan

Help for command '/site.scan':

Prototype: MEME.CLI::Int32 SiteScan(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /site.scan /query <LDM.xml> /subject <subject.fasta> [/out <outDIR>]
  Example:      MEME /site.scan

Help for command '/SiteHits.Footprints':

Prototype: MEME.CLI::Int32 SiteHitsToFootprints(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Generates the regulation information.
  Usage:        G:\GCModeller\manual\bin\MEME.exe /SiteHits.Footprints /sites <MotifSiteHits.Csv> /bbh <bbh.Csv> /meme <meme.txt_DIR> /PTT <genome.PTT> /DOOR <DOOR.opr> [/queryHash /out <out.csv>]
  Example:      MEME /SiteHits.Footprints

Help for command '/SWTOM.Compares':

Prototype: MEME.CLI::Int32 SWTomCompares(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /SWTOM.Compares /query <query.meme.txt> /subject <subject.meme.txt> [/out <outDIR> /no-HTML]
  Example:      MEME /SWTOM.Compares

Help for command '/SWTOM.Compares.Batch':

Prototype: MEME.CLI::Int32 SWTomComparesBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /SWTOM.Compares.Batch /query <query.meme.DIR> /subject <subject.meme.DIR> [/out <outDIR> /no-HTML]
  Example:      MEME /SWTOM.Compares.Batch

Help for command '/SWTOM.LDM':

Prototype: MEME.CLI::Int32 SWTomLDM(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /SWTOM.LDM /query <ldm.xml> /subject <ldm.xml> [/out <outDIR> /method <pcc/ed/sw; default:=pcc>]
  Example:      MEME /SWTOM.LDM

Help for command '/SWTOM.Query':

Prototype: MEME.CLI::Int32 SWTomQuery(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /SWTOM.Query /query <meme.txt> [/out <outDIR> /method <pcc> /bits.level 1.6 /minW 6 /no-HTML]
  Example:      MEME /SWTOM.Query

Parameters information:

       [/no-HTML]
    Description:  If this parameter is true, then only the XML result will be export.

    Example:      /no-HTML ""

Accepted Types

/no-HTML

Help for command '/SWTOM.Query.Batch':

Prototype: MEME.CLI::Int32 SWTomQueryBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /SWTOM.Query.Batch /query <meme.txt.DIR> [/out <outDIR> /SW-offset 0.6 /method <pcc> /bits.level 1.5 /minW 4 /SW-threshold 0.75 /tom-threshold 0.75 /no-HTML]
  Example:      MEME /SWTOM.Query.Batch

Parameters information:

       [/no-HTML]
    Description:  If this parameter is true, then only the XML result will be export.

    Example:      /no-HTML ""

Accepted Types

/no-HTML

Help for command '/Tom.Query':

Prototype: MEME.CLI::Int32 TomQuery(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Tom.Query /query <ldm.xml/meme.txt> [/out <outDIR> /method <pcc/ed; default:=pcc> /cost <0.7> /threshold <0.65> /meme]
  Example:      MEME /Tom.Query

Help for command '/Tom.Query.Batch':

Prototype: MEME.CLI::Int32 TomQueryBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Tom.Query.Batch /query <inDIR> [/out <outDIR> /method <pcc/ed; default:=pcc> /cost 0.7 /threshold <0.65>]
  Example:      MEME /Tom.Query.Batch

Help for command '/TomTOM':

Prototype: MEME.CLI::Int32 TomTOMMethod(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /TomTOM /query <meme.txt> /subject <LDM.xml> [/out <outDIR> /method <pcc/ed; default:=pcc> /cost <0.7> /threshold <0.3>]
  Example:      MEME /TomTOM

Help for command '/TomTom.LDM':

Prototype: MEME.CLI::Int32 LDMTomTom(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /TomTom.LDM /query <ldm.xml> /subject <ldm.xml> [/out <outDIR> /method <pcc/ed/sw; default:=sw> /cost <0.7> /threshold <0.65>]
  Example:      MEME /TomTom.LDM

Help for command '/TomTOM.Similarity':

Prototype: MEME.CLI::Int32 MEMEPlantSimilarity(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /TomTOM.Similarity /in <TOM_OUT.DIR> [/out <out.Csv>]
  Example:      MEME /TomTOM.Similarity

Help for command '/TOMTOM.Similarity.Batch':

Prototype: MEME.CLI::Int32 MEMEPlantSimilarityBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /TOMTOM.Similarity.Batch /in <inDIR> [/out <out.csv>]
  Example:      MEME /TOMTOM.Similarity.Batch

Help for command '/TomTom.Sites.Groups':

Prototype: MEME.CLI::Int32 ExportTOMSites(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /TomTom.Sites.Groups /in <similarity.csv> /meme <meme.DIR> [/grep <regex> /out <out.DIR>]
  Example:      MEME /TomTom.Sites.Groups

Help for command '/Trim.MastSite':

Prototype: MEME.CLI::Int32 Trim(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe /Trim.MastSite /in <mastSite.Csv> /locus <locus_tag> /correlations <DIR/name> [/out <out.csv> /cut <0.65>]
  Example:      MEME /Trim.MastSite

Help for command '--build.Regulations':

Prototype: MEME.CLI::Int32 Build(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Genome wide step 2
  Usage:        G:\GCModeller\manual\bin\MEME.exe --build.Regulations /bbh <regprecise.bbhMapped.csv> /mast <mastSites.csv> [/cutoff <0.6> /out <out.csv> /sp <spName> /DOOR <genome.opr> /DOOR.extract]
  Example:      MEME --build.Regulations

Parameters information:

       [/DOOR.extract]
    Description:  Extract the operon structure genes after assign the operon information.

    Example:      /DOOR.extract ""

Accepted Types

/DOOR.extract

Help for command '--build.Regulations.From.Motifs':

Prototype: MEME.CLI::Int32 BuildFromMotifSites(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --build.Regulations.From.Motifs /bbh <regprecise.bbhMapped.csv> /motifs <motifSites.csv> [/cutoff <0.6> /sp <spName> /out <out.csv>]
  Example:      MEME --build.Regulations.From.Motifs

Help for command '--CExpr.WGCNA':

Prototype: MEME.CLI::Int32 WGCNAModsCExpr(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --CExpr.WGCNA /mods <CytoscapeNodes.txt> /genome <genome.DIR|*.PTT;*.fna> /out <DIR.out>
  Example:      MEME --CExpr.WGCNA

Help for command 'Download.Regprecise':

Prototype: MEME.CLI::Int32 DownloadRegprecise2(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Download Regprecise database from Web API
  Usage:        G:\GCModeller\manual\bin\MEME.exe Download.Regprecise [/work ./ /save <saveXml>]
  Example:      MEME Download.Regprecise

Help for command '--Dump.KEGG.Family':

Prototype: MEME.CLI::Int32 KEGGFamilyDump(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --Dump.KEGG.Family /in <in.fasta> [/out <out.csv>]
  Example:      MEME --Dump.KEGG.Family

Parameters information:

    /in
    Description:  The RegPrecise formated title fasta file.

    Example:      /in ""

Accepted Types

/in

Help for command '--family.statics':

Prototype: MEME.CLI::Int32 FamilyStatics(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --family.statics /sites <motifSites.csv> /mods <directory.kegg_modules>
  Example:      MEME --family.statics

Help for command '--Get.Intergenic':

Prototype: MEME.CLI::Int32 GetIntergenic(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --Get.Intergenic /PTT <genome.ptt> /nt <genome.fasta> [/o <out.fasta> /len 100 /strict]
  Example:      MEME --Get.Intergenic

Help for command '--GetFasta':

Prototype: MEME.CLI::Int32 GetFasta(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --GetFasta /bbh <bbhh.csv> /id <subject_id> /regprecise <regprecise.fasta>
  Example:      MEME --GetFasta

Help for command '--hits.diff':

Prototype: MEME.CLI::Int32 DiffHits(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --hits.diff /query <bbhh.csv> /subject <bbhh.csv> [/reverse]
  Example:      MEME --hits.diff

Help for command '--Intersect.Max':

Prototype: MEME.CLI::Int32 MaxIntersection(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --Intersect.Max /query <bbhh.csv> /subject <bbhh.csv>
  Example:      MEME --Intersect.Max

Help for command '--logo.Batch':

Prototype: MEME.CLI::Int32 LogoBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --logo.Batch -in <inDIR> [/out <outDIR>]
  Example:      MEME --logo.Batch

Help for command '--mapped-Back':

Prototype: MEME.CLI::Int32 SiteMappedBack(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --mapped-Back /meme <meme.text> /mast <mast.xml> /ptt <genome.ptt> [/out <out.csv> /offset <10> /atg-dist <250>]
  Example:      MEME --mapped-Back

Help for command 'mast.compile':

Prototype: MEME.CLI::Int32 CompileMast(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe mast.compile /mast <mast.xml> /ptt <genome.ptt> [/no-meme /no-regInfo /p-value 1e-3 /mast-ldm <DIR default:=GCModeller/Regprecise/MEME/MAST_LDM> /atg-dist 250]
  Example:      MEME mast.compile

Help for command 'mast.compile.bulk':

Prototype: MEME.CLI::Int32 CompileMastBuck(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Genome wide step 1
  Usage:        G:\GCModeller\manual\bin\MEME.exe mast.compile.bulk /source <source_dir> [/ptt <genome.ptt> /atg-dist <500> /no-meme /no-regInfo /p-value 1e-3 /mast-ldm <DIR default:=GCModeller/Regprecise/MEME/MAST_LDM> /related.all]
  Example:      MEME mast.compile.bulk

Parameters information:

       [/no-meme]
    Description:  Specific that the mast site construction will without and meme pwm MAST_LDM model.

    Example:      /no-meme ""

Accepted Types

/no-meme

Help for command '--modules.regulates':

Prototype: MEME.CLI::Int32 ModuleRegulates(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Exports the Venn diagram model for the module regulations.
  Usage:        G:\GCModeller\manual\bin\MEME.exe --modules.regulates /in <virtualfootprints.csv> [/out <out.DIR> /mods <KEGG_modules.DIR>]
  Example:      MEME --modules.regulates

Parameters information:

    /in
    Description:  The footprints data required of fill out the pathway Class, category and type information before you call this function.
                   If the fields is blank, then your should specify the /mods parameter.

    Example:      /in ""

Accepted Types

/in

Help for command 'Motif.Locates':

Prototype: MEME.CLI::Int32 MotifLocites(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe Motif.Locates -ptt <bacterial_genome.ptt> -meme <meme.txt> [/out <out.csv>]
  Example:      MEME Motif.Locates

Help for command 'MotifScan':

Prototype: MEME.CLI::Int32 MotifScan(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Scan for the motif site by using fragment similarity.
  Usage:        G:\GCModeller\manual\bin\MEME.exe MotifScan -nt <nt.fasta> /motif <motifLDM.xml/LDM_Name/FamilyName> [/delta <default:80> /delta2 <default:70> /offSet <default:5> /out <saved.csv>]
  Example:      MEME MotifScan

Help for command '--pathway.regulates':

Prototype: MEME.CLI::Int32 PathwayRegulations(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Associates of the pathway regulation information for the predicted virtual footprint information.
  Usage:        G:\GCModeller\manual\bin\MEME.exe --pathway.regulates -footprints <virtualfootprint.csv> /pathway <DIR.KEGG.Pathways> [/out <./PathwayRegulations/>]
  Example:      MEME --pathway.regulates

Help for command 'Regprecise.Compile':

Prototype: MEME.CLI::Int32 CompileRegprecise(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  The repository parameter is a directory path which is the regprecise database root directory in the GCModeller directory, if you didn't know how to set this value, please leave it blank.
  Usage:        G:\GCModeller\manual\bin\MEME.exe Regprecise.Compile [<repository>]
  Example:      MEME Regprecise.Compile

Help for command 'regulators.bbh':

Prototype: MEME.CLI::Int32 RegulatorsBBh(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Compiles for the regulators in the bacterial genome mapped on the regprecise database using bbh method.
  Usage:        G:\GCModeller\manual\bin\MEME.exe regulators.bbh /bbh <bbhDIR/bbh.index.Csv> [/save <save.csv> /direct /regulons /maps <genome.gb>]
  Example:      MEME regulators.bbh

Parameters information:

       [/regulons]
    Description:  The data source of the /bbh parameter is comes from the regulons bbh data.

    Example:      /regulons ""

Accepted Types

/regulons

Help for command 'regulators.compile':

Prototype: MEME.CLI::Int32 RegulatorsCompile()

  Information:  Regprecise regulators data source compiler.
  Usage:        G:\GCModeller\manual\bin\MEME.exe 
  Example:      MEME regulators.compile

Help for command '--site.Match':

Prototype: MEME.CLI::Int32 SiteMatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --site.Match /meme <meme.text> /mast <mast.xml> /out <out.csv> [/ptt <genome.ptt> /len <150,200,250,300,350,400,450,500>]
  Example:      MEME --site.Match

Parameters information:

       [/len]
    Description:  If not specific this parameter, then the function will trying to parsing the length value from the meme text automatically.

    Example:      /len ""

Accepted Types

/len

Help for command '--site.Matches':

Prototype: MEME.CLI::Int32 SiteMatches(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --site.Matches /meme <DIR.meme.text> /mast <DIR.mast.xml> /out <out.csv> [/ptt <genome.ptt>]
  Example:      MEME --site.Matches

Help for command '--site.Matches.text':

Prototype: MEME.CLI::Int32 SiteMatchesText(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Using this function for processing the meme text output from the tmod toolbox.
  Usage:        G:\GCModeller\manual\bin\MEME.exe --site.Matches.text /meme <DIR.meme.text> /mast <DIR.mast.xml> /out <out.csv> [/ptt <genome.ptt> /fasta <original.fasta.DIR>]
  Example:      MEME --site.Matches.text

Help for command '--site.stat':

Prototype: MEME.CLI::Int32 SiteStat(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Statics of the PCC correlation distribution of the regulation
  Usage:        G:\GCModeller\manual\bin\MEME.exe --site.stat /in <footprints.csv> [/out <out.csv>]
  Example:      MEME --site.stat

Help for command '--TCS.Module.Regulations':

Prototype: MEME.CLI::Int32 TCSRegulateModule(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --TCS.Module.Regulations /MiST2 <MiST2.xml> /footprint <footprints.csv> /Pathways <KEGG_Pathways.DIR>
  Example:      MEME --TCS.Module.Regulations

Help for command '--TCS.Regulations':

Prototype: MEME.CLI::Int32 TCSRegulations(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\MEME.exe --TCS.Regulations /TCS <DIR.TCS.csv> /modules <DIR.mod.xml> /regulations <virtualfootprint.csv>
  Example:      MEME --TCS.Regulations

Help for command 'VirtualFootprint.DIP':

Prototype: MEME.CLI::Int32 VirtualFootprintDIP(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Associate the dip information with the Sigma 70 virtual footprints.
  Usage:        G:\GCModeller\manual\bin\MEME.exe VirtualFootprint.DIP vf.csv <csv> dip.csv <csv>
  Example:      MEME VirtualFootprint.DIP

Help for command 'wGet.Regprecise':

Prototype: MEME.CLI::Int32 DownloadRegprecise(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Download Regprecise database from REST API
  Usage:        G:\GCModeller\manual\bin\MEME.exe wGet.Regprecise [/repository-export <dir.export, default: ./> /updates]
  Example:      MEME wGet.Regprecise

MEME - SMRUCC/GCModeller GitHub Wiki

title: MEME tags: [maunal, tools] date: 7/27/2016 6:40:19 PM

GCModeller [version 1.34.0.2]

Commands

Help for command '/BBH.Select.Regulators':

Help for command '/Build.FamilyDb':

Help for command '/Copys':

Help for command '/Copys.DIR':

Help for command '/CORN':

Help for command '/EXPORT.MotifDraws':

Help for command '/Export.MotifSites':

Help for command '/Export.Regprecise.Motifs':

Help for command '/Export.Similarity.Hits':

Help for command '/Footprints':

Accepted Types

/extract

Help for command '/Hits.Context':

Help for command '/LDM.Compares':

Help for command '/LDM.MaxW':

Help for command '/LDM.Selects':

Help for command '/MAST.MotifMatches':

Help for command '/MAST.MotifMatchs.Family':

Help for command '/mast.Regulations':

Help for command '/MAST_LDM.Build':

Help for command '/MEME.Batch':

Accepted Types

/in

/out

Help for command '/MEME.LDMs':

Help for command '/Motif.BuildRegulons':

Help for command '/Motif.Info':

Accepted Types

/loci

/motifs

Help for command '/Motif.Info.Batch':

Accepted Types

/motifs

/num_threads

Help for command '/Motif.Similarity':

Help for command '/MotifHits.Regulation':

Help for command '/Parser.DEGs':

Help for command '/Parser.Locus':

Help for command '/Parser.Log2':

Help for command '/Parser.MAST':

Help for command '/Parser.Modules':

Help for command '/Parser.Operon':

Accepted Types

/family

Help for command '/Parser.Pathway':

Help for command '/Parser.RegPrecise.Operons':

Help for command '/Parser.Regulon':

Help for command '/Parser.Regulon.gb':

Help for command '/Parser.Regulon.Merged':

Help for command '/Regulator.Motifs':

Help for command '/Regulator.Motifs.Test':

Help for command '/regulon.export':

Help for command '/Regulon.Reconstruct':

Help for command '/Regulon.Reconstruct2':

Help for command '/Regulon.Reconstructs':

Accepted Types

/bbh

/genome

/door

Help for command '/Regulon.Test':

Help for command '/RfamSites':

Help for command '/seq.logo':

Help for command '/Similarity.Union':

Help for command '/Site.MAST_Scan':

Accepted Types

/batch

Help for command '/Site.MAST_Scan.Batch':

Help for command '/Site.RegexScan':

Help for command '/site.scan':

Help for command '/SiteHits.Footprints':

Help for command '/SWTOM.Compares':

Help for command '/SWTOM.Compares.Batch':

Help for command '/SWTOM.LDM':

Help for command '/SWTOM.Query':

Accepted Types

/no-HTML

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