Information:  Install NCBI CDD database into the GCModeller repository database for the MPAlignment analysis.
  Usage:        G:\GCModeller\manual\bin\mpl.exe /Build.Db.CDD /source <source.DIR>
  Example:      mpl /Build.Db.CDD 

  Information:  Build protein family database from KEGG database dump data and using for the protein family annotation by MPAlignment.
  Usage:        G:\GCModeller\manual\bin\mpl.exe /Build.Db.Family /source <source.KEGG.fasta> /pfam <pfam-string.csv>
  Example:      mpl /Build.Db.Family 

  Information:  
  Usage:        G:\GCModeller\manual\bin\mpl.exe /Build.Db.Family.Manual-Build /pfam-string <pfam-string.csv> /name <familyName>
  Example:      mpl /Build.Db.Family.Manual-Build 

  Information:  Build protein functional orthology database from KEGG orthology or NCBI COG database.
  Usage:        G:\GCModeller\manual\bin\mpl.exe /Build.Db.Ortholog [/COG <cogDIR> /KO]
  Example:      mpl /Build.Db.Ortholog 

  Information:  Build protein interaction seeds database from string-db.
  Usage:        G:\GCModeller\manual\bin\mpl.exe 
  Example:      mpl /Build.Db.PPI 

  Information:  
  Usage:        G:\GCModeller\manual\bin\mpl.exe /Build.PPI.Signature /in <clustalW.fasta> [/level <5> /out <out.xml>]
  Example:      mpl /Build.PPI.Signature 

       [/level]
    Description:  It is not recommended to modify this value. The greater of this value, the more strict of the interaction scoring. level 5 is enough.

    Example:      /level ""

  Information:  
  Usage:        G:\GCModeller\manual\bin\mpl.exe /KEGG.Family /in <inDIR> /pfam <pfam-string.csv> [/out <out.csv>]
  Example:      mpl /KEGG.Family 

  Information:  
  Usage:        G:\GCModeller\manual\bin\mpl.exe /Motif.Density /in <pfam-string.csv> [/out <out.csv>]
  Example:      mpl /Motif.Density 

  Information:  Align your proteins with selected protein domain structure database by using blast+ program.
  Usage:        G:\GCModeller\manual\bin\mpl.exe /Pfam.Align /query <query.fasta> [/db <name/path> /out <blastOut.txt>]
  Example:      mpl /Pfam.Align 

  Information:  
  Usage:        G:\GCModeller\manual\bin\mpl.exe /Pfam.Sub /index <bbh_index.csv> /pfam <pfam-string> [/out <sub-out.csv>]
  Example:      mpl /Pfam.Sub 

  Information:  Dump the pfam-String domain Structure composition information from the blastp alignment result.
  Usage:        G:\GCModeller\manual\bin\mpl.exe /Pfam-String.Dump /In <blastp_out.txt> [/out <pfam-String.csv> /evalue <0.001> /identities <0.2> /coverage <0.85>]
  Example:      mpl /Pfam-String.Dump 

    /In
    Description:  The blastp output For the protein alignment, which the aligned database can be selected from Pfam-A Or NCBI CDD. And blast+ program Is recommended For used For the domain alignment.

    Example:      /In ""

   [/out]
    Description:  The output Excel .csv data file path For the dumped pfam-String data Of your annotated protein. If this parameter Is empty, Then the file will saved On the same location With your blastp input file.

    Example:      /out ""

  Information:  
  Usage:        G:\GCModeller\manual\bin\mpl.exe /Select.Pfam-String /in <pfam-string.csv> /hits <bbh/sbh.csv> [/hit_name /out <out.csv>]
  Example:      mpl /Select.Pfam-String 

  Information:  MPAlignment on your own dataset.
  Usage:        G:\GCModeller\manual\bin\mpl.exe --align /query <pfam-string.csv> /subject <pfam-string.csv> [/hits <query_vs_sbj.blastp.csv> /flip-bbh /out <alignment_out.csv> /mp <cutoff:=0.65> /swap /parts]
  Example:      mpl --align 

       [/swap]
    Description:  Swap the location of query and subject in the output result set.

    Example:      /swap ""

   [/parts]
    Description:  Does the domain motif equals function determine the domain positioning equals just if one side in the high scoring then thoese two domain its position is equals? 
Default is not, default checks right side and left side.

    Example:      /parts ""

   [/flip-bbh]
    Description:  Swap the direction of the query_name/hit_name in the hits?

    Example:      /flip-bbh ""

  Information:  Protein family annotation by using MPAlignment algorithm.
  Usage:        G:\GCModeller\manual\bin\mpl.exe --align.Family /query <pfam-string.csv> [/out <out.csv> /threshold 0.5 /mp 0.6 /Name <null>]
  Example:      mpl --align.Family 

       [/Name]
    Description:  The database name of the aligned subject, if this value is empty or not exists in the source, then the entired Family database will be used.

    Example:      /Name ""

  Information:  
  Usage:        G:\GCModeller\manual\bin\mpl.exe --align.Family_test /query <pfam-string> /name <dbName/Path> [/threshold <0.65> /mpCut <0.65> /accept <10>]
  Example:      mpl --align.Family_test 

  Information:  Protein function annotation by using MPAlignment algorithm.
  Usage:        G:\GCModeller\manual\bin\mpl.exe 
  Example:      mpl --align.Function 

  Information:  Protein-Protein interaction network annotation by using MPAlignment algorithm.
  Usage:        G:\GCModeller\manual\bin\mpl.exe 
  Example:      mpl --align.PPI 

  Information:  
  Usage:        G:\GCModeller\manual\bin\mpl.exe --align.PPI_test /query <contacts.fasta> /db <ppi_signature.Xml> [/mp <cutoff:=0.9> /out <outDIR>]
  Example:      mpl --align.PPI_test 

  Information:  MPAlignment test, pfam-string value must be in format as  <locusId>:<length>:<pfam-string>
  Usage:        G:\GCModeller\manual\bin\mpl.exe --align.String /query <pfam-string> /subject <pfam-string> [/mp <cutoff:=0.65> /out <outDIR> /parts]
  Example:      mpl --align.String 

  Information:  
  Usage:        G:\GCModeller\manual\bin\mpl.exe --blast.allhits /blast <blastp.txt> [/out <sbh.csv> /coverage <0.5> /identities 0.15]
  Example:      mpl --blast.allhits 

  Information:  
  Usage:        G:\GCModeller\manual\bin\mpl.exe --View.Alignment /blast <blastp.txt> /name <queryName> [/out <out.png>]
  Example:      mpl --View.Alignment