PhenoTree - SMRUCC/GCModeller GitHub Wiki

title: PhenoTree tags: [maunal, tools] date: 7/27/2016 6:40:21 PM

GCModeller [version 1.0.0.0]

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

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

Function API Info
/Cluster.Genes.Phenotype
/Parts.COGs
/venn.Matrix

Commands

Help for command '/Cluster.Genes.Phenotype':

Prototype: PhenoTree.CLI::Int32 GenePhenoClusters(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\PhenoTree.exe /Cluster.Genes.Phenotype /sites <motifSites.csv> [/out <out.tree_cluster.csv> /parallel]
  Example:      PhenoTree /Cluster.Genes.Phenotype
Help for command '/Parts.COGs':

Prototype: PhenoTree.CLI::Int32 PartitioningCOGs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\PhenoTree.exe /Parts.COGs /cluster <btree.clusters.csv> /myva <COGs.csv> [/depth <-1> /out <EXPORT_DIR>]
  Example:      PhenoTree /Parts.COGs
Help for command '/venn.Matrix':

Prototype: PhenoTree.CLI::Int32 VennMatrix(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\PhenoTree.exe /venn.Matrix /besthits <besthits.xml.DIR> [/query <sp.name> /limits -1 /out <out.txt>]
  Example:      PhenoTree /venn.Matrix

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