1. 1. GCModeller [version 3.0.2456.4506]
    1. 1.1. Commands
      1. 1.1.0.0.1. Help for command ‘/align’:
      2. 1.1.0.0.2. Help for command ‘/Clustal.Cut’:
      3. 1.1.0.0.3. Help for command ‘/Distinct’:
      4. 1.1.0.0.4. Help for command ‘/Get.Locis’:
      5. 1.1.0.0.5. Help for command ‘/Gff.Sites’:
      6. 1.1.0.0.6. Help for command ‘/gwANI’:
      7. 1.1.0.0.7. Help for command ‘/Loci.describ’:
      8. 1.1.0.0.8. Help for command ‘/logo’:
    2. 1.1.0.1. Accepted Types
      1. 1.1.0.1.1. /in
      2. 1.1.0.1.2. /out
      3. 1.1.0.1.3. /title
      4. 1.1.0.1.4. Help for command ‘/Merge’:
      5. 1.1.0.1.5. Help for command ‘/Mirror.Batch’:
    3. 1.1.0.2. Accepted Types
      1. 1.1.0.2.1. /nt
      2. 1.1.0.2.2. /mp
      3. 1.1.0.2.3. Help for command ‘/Mirror.Fuzzy’:
    4. 1.1.0.3. Accepted Types
      1. 1.1.0.3.1. /in
      2. 1.1.0.3.2. /out
      3. 1.1.0.3.3. Help for command ‘/Mirror.Fuzzy.Batch’:
      4. 1.1.0.3.4. Help for command ‘/Mirror.Vector’:
      5. 1.1.0.3.5. Help for command ‘/Mirrors.Context’:
    5. 1.1.0.4. Accepted Types
      1. 1.1.0.4.1. /trans
      2. 1.1.0.4.2. Help for command ‘/Mirrors.Group’:
    6. 1.1.0.5. Accepted Types
      1. 1.1.0.5.1. /fuzzy
      2. 1.1.0.5.2. Help for command ‘/Mirrors.Group.Batch’:
      3. 1.1.0.5.3. Help for command ‘/Mirrors.Nt.Trim’:
      4. 1.1.0.5.4. Help for command ‘/nw’:
    7. 1.1.0.6. Accepted Types
      1. 1.1.0.6.1. /query
      2. 1.1.0.6.2. /subject
      3. 1.1.0.6.3. /out
      4. 1.1.0.6.4. Help for command ‘/Palindrome.BatchTask’:
    8. 1.1.0.7. Accepted Types
      1. 1.1.0.7.1. /Palindrome
      2. 1.1.0.7.2. Help for command ‘/Palindrome.Screen.MaxMatches’:
      3. 1.1.0.7.3. Help for command ‘/Palindrome.Screen.MaxMatches.Batch’:
      4. 1.1.0.7.4. Help for command ‘/Palindrome.Workflow’:
    9. 1.1.0.8. Accepted Types
      1. 1.1.0.8.1. /in
      2. 1.1.0.8.2. /Palindrome
      3. 1.1.0.8.3. Help for command ‘/Select.By_Locus’:
      4. 1.1.0.8.4. Help for command ‘/Sigma’:
      5. 1.1.0.8.5. Help for command ‘/SimpleSegment.AutoBuild’:
    10. 1.1.0.9. Accepted Types
      1. 1.1.0.9.1. /in
      2. 1.1.0.9.2. /out
      3. 1.1.0.9.3. Help for command ‘/SimpleSegment.Mirrors’:
    11. 1.1.0.10. Accepted Types
      1. 1.1.0.10.1. /in
      2. 1.1.0.10.2. /out
      3. 1.1.0.10.3. Help for command ‘/SimpleSegment.Mirrors.Batch’:
      4. 1.1.0.10.4. Help for command ‘/SNP’:
    12. 1.1.0.11. Accepted Types
      1. 1.1.0.11.1. /in
      2. 1.1.0.11.2. /ref
      3. 1.1.0.11.3. /pure
      4. 1.1.0.11.4. Help for command ‘/Split’:
      5. 1.1.0.11.5. Help for command ‘/subset’:
      6. 1.1.0.11.6. Help for command ‘/Time.Diffs’:
      7. 1.1.0.11.7. Help for command ‘/To_Fasta’:
      8. 1.1.0.11.8. Help for command ‘/Write.Seeds’:
      9. 1.1.0.11.9. Help for command ‘-321’:
      10. 1.1.0.11.10. Help for command ‘–align’:
      11. 1.1.0.11.11. Help for command ‘–align.Self’:
      12. 1.1.0.11.12. Help for command ‘-complement’:
      13. 1.1.0.11.13. Help for command ‘–Drawing.ClustalW’:
      14. 1.1.0.11.14. Help for command ‘–Hairpinks’:
      15. 1.1.0.11.15. Help for command ‘–Hairpinks.batch.task’:
      16. 1.1.0.11.16. Help for command ‘–ImperfectsPalindrome.batch.Task’:
      17. 1.1.0.11.17. Help for command ‘–Mirror.From.Fasta’:
    13. 1.1.0.12. Accepted Types
      1. 1.1.0.12.1. /nt
      2. 1.1.0.12.2. Help for command ‘–Mirror.From.NT’:
      3. 1.1.0.12.3. Help for command ‘–Palindrome.batch.Task’:
      4. 1.1.0.12.4. Help for command ‘–Palindrome.From.FASTA’:
    14. 1.1.0.13. Accepted Types
      1. 1.1.0.13.1. /nt
      2. 1.1.0.13.2. /out
      3. 1.1.0.13.3. Help for command ‘–Palindrome.From.NT’:
      4. 1.1.0.13.4. Help for command ‘–Palindrome.Imperfects’:
      5. 1.1.0.13.5. Help for command ‘-pattern_search’:
    15. 1.1.0.14. Accepted Types
      1. 1.1.0.14.1. -i
      2. 1.1.0.14.2. -p
      3. 1.1.0.14.3. -o
      4. 1.1.0.14.4. -f
      5. 1.1.0.14.5. Help for command ‘–PerfectPalindrome.Filtering’:
      6. 1.1.0.14.6. Help for command ‘Repeats.Density’:
      7. 1.1.0.14.7. Help for command ‘-reverse’:
      8. 1.1.0.14.8. Help for command ‘rev-Repeats.Density’:
      9. 1.1.0.14.9. Help for command ‘Search.Batch’:
    16. 1.1.0.15. Accepted Types
      1. 1.1.0.15.1. /aln
      2. 1.1.0.15.2. Help for command ‘-segment’:
      3. 1.1.0.15.3. Help for command ‘–segments’:
    17. 1.1.0.16. Accepted Types
      1. 1.1.0.16.1. /reversed
      2. 1.1.0.16.2. /complement
      3. 1.1.0.16.3. /brief-dump
      4. 1.1.0.16.4. Help for command ‘–ToVector’:
      5. 1.1.0.16.5. Help for command ‘–translates’:
    18. 1.1.0.17. Accepted Types
      1. 1.1.0.17.1. /orf
      2. 1.1.0.17.2. /force
      3. 1.1.0.17.3. /transl_table
      4. 1.1.0.17.4. Help for command ‘–Trim’:
    19. 1.1.0.18. Accepted Types
      1. 1.1.0.18.1. /case
      2. 1.1.0.18.2. /break

GCModeller [version 3.0.2456.4506]

Module AssemblyName: file:///G:/GCModeller/manual/bin/seqtools.exe
Root namespace: seqtools.Utilities

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

Function API Info
/align
/Clustal.Cut
/Distinct
/Get.Locis
/Gff.Sites
/gwANI
/Loci.describ Testing
/logo * Drawing the sequence logo from the clustal alignment result.
/Merge Only search for 1 level folder, dit not search receve.
/Mirror.Batch
/Mirror.Fuzzy
/Mirror.Fuzzy.Batch
/Mirror.Vector
/Mirrors.Context This function will convert the mirror data to the simple segment object data
/Mirrors.Group
/Mirrors.Group.Batch
/Mirrors.Nt.Trim
/nw RunNeedlemanWunsch
/Palindrome.BatchTask
/Palindrome.Screen.MaxMatches
/Palindrome.Screen.MaxMatches.Batch
/Palindrome.Workflow
/Select.By_Locus
/Sigma
/SimpleSegment.AutoBuild
/SimpleSegment.Mirrors
/SimpleSegment.Mirrors.Batch
/SNP
/Split
/subset
/Time.Diffs
/To_Fasta Convert the sequence data in a excel annotation file into a fasta sequence file.
/Write.Seeds
-321 Polypeptide sequence 3 letters to 1 lettes sequence.
–align
–align.Self
-complement
–Drawing.ClustalW
–Hairpinks
–Hairpinks.batch.task
–ImperfectsPalindrome.batch.Task
–Mirror.From.Fasta Mirror Palindrome, search from a fasta file.
–Mirror.From.NT Mirror Palindrome, and this function is for the debugging test
–Palindrome.batch.Task
–Palindrome.From.FASTA
–Palindrome.From.NT This function is just for debugger test, /nt parameter is the nucleotide sequence data as ATGCCCC
–Palindrome.Imperfects
-pattern_search Parsing the sequence segment from the sequence source using regular expression.
–PerfectPalindrome.Filtering
Repeats.Density
-reverse
rev-Repeats.Density
Search.Batch Batch search for repeats.
-segment
–segments
–ToVector
–translates Translates the ORF gene as protein sequence. If any error was output from the console, please using > operator dump the output to a log file for the analysis.
–Trim

Commands


Help for command ‘/align’:

Prototype: seqtools.Utilities::Int32 Align2(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /align /query <query.fasta> /subject <subject.fasta> [/blosum <matrix.txt> /out <out.xml>]
Example: seqtools /align
Help for command ‘/Clustal.Cut’:

Prototype: seqtools.Utilities::Int32 CutMlAlignment(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Clustal.Cut /in <in.fasta> [/left 0.1 /right 0.1 /out <out.fasta>]
Example: seqtools /Clustal.Cut
Help for command ‘/Distinct’:

Prototype: seqtools.Utilities::Int32 Distinct(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Distinct /in <in.fasta> [/out <out.fasta>]
Example: seqtools /Distinct
Help for command ‘/Get.Locis’:

Prototype: seqtools.Utilities::Int32 GetSimpleSegments(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Get.Locis /in <locis.csv> /nt <genome.nt.fasta> [/out <outDIR>]
Example: seqtools /Get.Locis
Help for command ‘/Gff.Sites’:

Prototype: seqtools.Utilities::Int32 GffSites(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Gff.Sites /fna <genomic.fna> /gff <genome.gff> [/out <out.fasta>]
Example: seqtools /Gff.Sites
Help for command ‘/gwANI’:

Prototype: seqtools.Utilities::Int32 gwANI(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /gwANI /in <in.fasta> [/fast /out <out.Csv>]
Example: seqtools /gwANI
Help for command ‘/Loci.describ’:

Prototype: seqtools.Utilities::Int32 LociDescript(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Testing
Usage: G:\GCModeller\manual\bin\seqtools.exe /Loci.describ /ptt <genome-context.ptt> [/test <loci:randomize> /complement /unstrand]
Example: seqtools /Loci.describ
Help for command ‘/logo’:

Prototype: seqtools.Utilities::Int32 SequenceLogo(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  * Drawing the sequence logo from the clustal alignment result.
Usage: G:\GCModeller\manual\bin\seqtools.exe /logo /in <clustal.fasta> [/out <out.png> /title ""]
Example: seqtools /logo

Parameters information:

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 /in
Description: The file path of the clustal output fasta file.

Example: /in ""

[/out]
Description: The output sequence logo image file path. default is the same name as the input fasta sequence file.

Example: /out ""

[/title]
Description: The display title on the sequence logo, default is using the fasta file name.

Example: /title ""

Accepted Types

/in

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaFile
Example:

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[

]

/out
/title
Help for command ‘/Merge’:

Prototype: seqtools.Utilities::Int32 Merge(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Only search for 1 level folder, dit not search receve.
Usage: G:\GCModeller\manual\bin\seqtools.exe /Merge /in <fasta.DIR> [/out <out.fasta> /trim /unique /ext <*.fasta> /brief]
Example: seqtools /Merge
Help for command ‘/Mirror.Batch’:

Prototype: seqtools.Utilities::Int32 MirrorBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Mirror.Batch /nt <nt.fasta> [/out <out.csv> /mp /min <3> /max <20> /num_threads <-1>]
Example: seqtools /Mirror.Batch

Parameters information:

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 /nt
Description:
Example: /nt ""

[/mp]
Description: Calculation in the multiple process mode?

Example: /mp ""

Accepted Types

/nt

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaFile
Example:

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[

]

/mp

Decalre: System.Boolean
Example:

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true

Help for command ‘/Mirror.Fuzzy’:

Prototype: seqtools.Utilities::Int32 FuzzyMirrors(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Mirror.Fuzzy /in <in.fasta> [/out <out.csv> /cut 0.6 /max-dist 6 /min 3 /max 20]
Example: seqtools /Mirror.Fuzzy

Parameters information:

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 /in
Description:
Example: /in ""

[/out]
Description:
Example: /out ""

Accepted Types

/in

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken
Example:

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{
"Extension": {
"DynamicHash": {
"Properties": [

],
"source": [

]
}
},
"SequenceData": "System.String",
"Attributes": [
"System.String"
]
}

/out

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci
Example:

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{
"Loci": "System.String",
"MirrorSite": "System.String",
"PalEnd": 0,
"Palindrome": "System.String",
"Start": 0
}

Help for command ‘/Mirror.Fuzzy.Batch’:

Prototype: seqtools.Utilities::Int32 FuzzyMirrorsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Mirror.Fuzzy.Batch /in <in.fasta/DIR> [/out <out.DIR> /cut 0.6 /max-dist 6 /min 3 /max 20 /num_threads <-1>]
Example: seqtools /Mirror.Fuzzy.Batch
Help for command ‘/Mirror.Vector’:

Prototype: seqtools.Utilities::Int32 MirrorsVector(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Mirror.Vector /in <inDIR> /size <genome.size> [/out out.txt]
Example: seqtools /Mirror.Vector
Help for command ‘/Mirrors.Context’:

Prototype: seqtools.Utilities::Int32 MirrorContext(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  This function will convert the mirror data to the simple segment object data
Usage: G:\GCModeller\manual\bin\seqtools.exe /Mirrors.Context /in <mirrors.csv> /PTT <genome.ptt> [/trans /strand <+/-> /out <out.csv> /stranded /dist <500bp>]
Example: seqtools /Mirrors.Context

Parameters information:

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   [/trans]
Description: Enable this option will using genome_size minus loci location for the location correction, only works in reversed strand.

Example: /trans ""

Accepted Types

/trans
Help for command ‘/Mirrors.Group’:

Prototype: seqtools.Utilities::Int32 MirrorGroups(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Mirrors.Group /in <mirrors.Csv> [/batch /fuzzy <-1> /out <out.DIR>]
Example: seqtools /Mirrors.Group

Parameters information:

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   [/fuzzy]
Description: -1 means group sequence by string equals compared, and value of 0-1 means using string fuzzy compare.

Example: /fuzzy ""

Accepted Types

/fuzzy
Help for command ‘/Mirrors.Group.Batch’:

Prototype: seqtools.Utilities::Int32 MirrorGroupsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Mirrors.Group.Batch /in <mirrors.DIR> [/fuzzy <-1> /out <out.DIR> /num_threads <-1>]
Example: seqtools /Mirrors.Group.Batch
Help for command ‘/Mirrors.Nt.Trim’:

Prototype: seqtools.Utilities::Int32 TrimNtMirrors(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Mirrors.Nt.Trim /in <mirrors.Csv> [/out <out.Csv>]
Example: seqtools /Mirrors.Nt.Trim
Help for command ‘/nw’:

Prototype: seqtools.Utilities::Int32 NW(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  RunNeedlemanWunsch
Usage: G:\GCModeller\manual\bin\seqtools.exe /nw /query <query.fasta> /subject <subject.fasta> [/out <out.txt>]
Example: seqtools /nw

Parameters information:

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    /query
Description:
Example: /query ""

/subject
Description:
Example: /subject ""

[/out]
Description:
Example: /out ""

Accepted Types

/query

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken
Example:

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{
"Extension": {
"DynamicHash": {
"Properties": [

],
"source": [

]
}
},
"SequenceData": "System.String",
"Attributes": [
"System.String"
]
}

/subject

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken
Example:

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{
"Extension": {
"DynamicHash": {
"Properties": [

],
"source": [

]
}
},
"SequenceData": "System.String",
"Attributes": [
"System.String"
]
}

/out

Decalre: System.String
Example:

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"System.String"

Help for command ‘/Palindrome.BatchTask’:

Prototype: seqtools.Utilities::Int32 PalindromeBatchTask(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Palindrome.BatchTask /in <in.DIR> [/num_threads 4 /min 3 /max 20 /min-appears 2 /cutoff <0.6> /Palindrome /max-dist <1000 (bp)> /partitions <-1> /out <out.DIR>]
Example: seqtools /Palindrome.BatchTask

Parameters information:

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   [/Palindrome]
Description: Only search for Palindrome, not includes the repeats data.

Example: /Palindrome ""

Accepted Types

/Palindrome
Help for command ‘/Palindrome.Screen.MaxMatches’:

Prototype: seqtools.Utilities::Int32 FilteringMatches(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Palindrome.Screen.MaxMatches /in <in.csv> /min <min.max-matches> [/out <out.csv>]
Example: seqtools /Palindrome.Screen.MaxMatches
Help for command ‘/Palindrome.Screen.MaxMatches.Batch’:

Prototype: seqtools.Utilities::Int32 FilteringMatchesBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Palindrome.Screen.MaxMatches.Batch /in <inDIR> /min <min.max-matches> [/out <out.DIR> /num_threads <-1>]
Example: seqtools /Palindrome.Screen.MaxMatches.Batch
Help for command ‘/Palindrome.Workflow’:

Prototype: seqtools.Utilities::Int32 PalindromeWorkflow(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Palindrome.Workflow /in <in.fasta> [/batch /min-appears 2 /min 3 /max 20 /cutoff <0.6> /max-dist <1000 (bp)> /Palindrome /partitions <-1> /out <out.DIR>]
Example: seqtools /Palindrome.Workflow

Parameters information:

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 /in
Description: This is a single sequence fasta file.

Example: /in ""

[/Palindrome]
Description: Only search for Palindrome, not includes the repeats data.

Example: /Palindrome ""

Accepted Types

/in
/Palindrome
Help for command ‘/Select.By_Locus’:

Prototype: seqtools.Utilities::Int32 SelectByLocus(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Select.By_Locus /in <locus.txt> /fa <fasta.inDIR> [/out <out.fasta>]
Example: seqtools /Select.By_Locus
Help for command ‘/Sigma’:

Prototype: seqtools.Utilities::Int32 Sigma(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Sigma /in <in.fasta> [/out <out.Csv> /simple /round <-1>]
Example: seqtools /Sigma
Help for command ‘/SimpleSegment.AutoBuild’:

Prototype: seqtools.Utilities::Int32 ConvertsAuto(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /SimpleSegment.AutoBuild /in <locis.csv> [/out <out.csv>]
Example: seqtools /SimpleSegment.AutoBuild

Parameters information:

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 /in
Description:
Example: /in ""

[/out]
Description:
Example: /out ""

Accepted Types

/in

Decalre: Microsoft.VisualBasic.DocumentFormat.Csv.DocumentStream.File
Example:

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[

]

/out

Decalre: SMRUCC.genomics.SequenceModel.NucleotideModels.SimpleSegment
Example:

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{
"Complement": "System.String",
"Ends": 0,
"ID": "System.String",
"SequenceData": "System.String",
"Start": 0,
"Strand": "System.String"
}

Help for command ‘/SimpleSegment.Mirrors’:

Prototype: seqtools.Utilities::Int32 ConvertMirrors(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /SimpleSegment.Mirrors /in <in.csv> [/out <out.csv>]
Example: seqtools /SimpleSegment.Mirrors

Parameters information:

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 /in
Description:
Example: /in ""

[/out]
Description:
Example: /out ""

Accepted Types

/in

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci
Example:

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{
"Loci": "System.String",
"MirrorSite": "System.String",
"PalEnd": 0,
"Palindrome": "System.String",
"Start": 0
}

/out

Decalre: SMRUCC.genomics.SequenceModel.NucleotideModels.SimpleSegment
Example:

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{
"Complement": "System.String",
"Ends": 0,
"ID": "System.String",
"SequenceData": "System.String",
"Start": 0,
"Strand": "System.String"
}

Help for command ‘/SimpleSegment.Mirrors.Batch’:

Prototype: seqtools.Utilities::Int32 ConvertMirrorsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /SimpleSegment.Mirrors.Batch /in <in.DIR> [/out <out.DIR>]
Example: seqtools /SimpleSegment.Mirrors.Batch
Help for command ‘/SNP’:

Prototype: seqtools.Utilities::Int32 SNP(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /SNP /in <nt.fasta> [/ref 0 /pure /monomorphic]
Example: seqtools /SNP

Parameters information:

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 /in
Description:

Example: /in ""

[/ref]
Description:
Example: /ref ""

[/pure]
Description:
Example: /pure ""

Accepted Types

/in

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaFile
Example:

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[

]

/ref

Decalre: System.Int32
Example:

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0

/pure

Decalre: System.Boolean
Example:

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true

Help for command ‘/Split’:

Prototype: seqtools.Utilities::Int32 Split(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Split /in <in.fasta> [/n <4096> /out <outDIR>]
Example: seqtools /Split
Help for command ‘/subset’:

Prototype: seqtools.Utilities::Int32 SubSet(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /subset /lstID <lstID.txt> /fa <source.fasta>
Example: seqtools /subset
Help for command ‘/Time.Diffs’:

Prototype: seqtools.Utilities::Int32 TimeDiffs(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Time.Diffs /in <aln.fasta> [/out <out.csv>]
Example: seqtools /Time.Diffs
Help for command ‘/To_Fasta’:

Prototype: seqtools.Utilities::Int32 ToFasta(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Convert the sequence data in a excel annotation file into a fasta sequence file.
Usage: G:\GCModeller\manual\bin\seqtools.exe /To_Fasta /in <anno.csv> [/out <out.fasta> /attrs <gene;locus_tag;gi;location,...> /seq <Sequence>]
Example: seqtools /To_Fasta
Help for command ‘/Write.Seeds’:

Prototype: seqtools.Utilities::Int32 WriteSeeds(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe /Write.Seeds /out <out.dat> [/prot /max <20>]
Example: seqtools /Write.Seeds
Help for command ‘-321’:

Prototype: seqtools.Utilities::Int32 PolypeptideBriefs(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Polypeptide sequence 3 letters to 1 lettes sequence.
Usage: G:\GCModeller\manual\bin\seqtools.exe -321 /in <sequence.txt> [/out <out.fasta>]
Example: seqtools -321
Help for command ‘–align’:

Prototype: seqtools.Utilities::Int32 Align(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --align /query <query.fasta> /subject <subject.fasta> [/out <out.DIR> /cost <0.7>]
Example: seqtools --align
Help for command ‘–align.Self’:

Prototype: seqtools.Utilities::Int32 AlignSelf(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --align.Self /query <query.fasta> /out <out.DIR> [/cost 0.75]
Example: seqtools --align.Self
Help for command ‘-complement’:

Prototype: seqtools.Utilities::Int32 Complement(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe -complement -i <input_fasta> [-o <output_fasta>]
Example: seqtools -complement
Help for command ‘–Drawing.ClustalW’:

Prototype: seqtools.Utilities::Int32 DrawClustalW(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --Drawing.ClustalW /in <align.fasta> [/out <out.png> /dot.Size 10]
Example: seqtools --Drawing.ClustalW
Help for command ‘–Hairpinks’:

Prototype: seqtools.Utilities::Int32 Hairpinks(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --Hairpinks /in <in.fasta> [/out <out.csv> /min <6> /max <7> /cutoff 3 /max-dist <35 (bp)>]
Example: seqtools --Hairpinks
Help for command ‘–Hairpinks.batch.task’:

Prototype: seqtools.Utilities::Int32 HairpinksBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --Hairpinks.batch.task /in <in.fasta> [/out <outDIR> /min <6> /max <7> /cutoff <0.6> /max-dist <35 (bp)> /num_threads <-1>]
Example: seqtools --Hairpinks.batch.task
Help for command ‘–ImperfectsPalindrome.batch.Task’:

Prototype: seqtools.Utilities::Int32 BatchSearchImperfectsPalindrome(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --ImperfectsPalindrome.batch.Task /in <in.fasta> /out <outDir> [/min <3> /max <20> /cutoff <0.6> /max-dist <1000 (bp)> /num_threads <-1>]
Example: seqtools --ImperfectsPalindrome.batch.Task
Help for command ‘–Mirror.From.Fasta’:

Prototype: seqtools.Utilities::Int32 SearchMirrotFasta(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Mirror Palindrome, search from a fasta file.
Usage: G:\GCModeller\manual\bin\seqtools.exe --Mirror.From.Fasta /nt <nt-sequence.fasta> [/out <out.csv> /min <3> /max <20>]
Example: seqtools --Mirror.From.Fasta

Parameters information:

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/nt
Description: This fasta file should contains only just one sequence.

Example: /nt ""

Accepted Types

/nt

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken
Example:

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{
"Extension": {
"DynamicHash": {
"Properties": [

],
"source": [

]
}
},
"SequenceData": "System.String",
"Attributes": [
"System.String"
]
}

Help for command ‘–Mirror.From.NT’:

Prototype: seqtools.Utilities::Int32 SearchMirrotNT(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Mirror Palindrome, and this function is for the debugging test
Usage: G:\GCModeller\manual\bin\seqtools.exe --Mirror.From.NT /nt <nt-sequence> /out <out.csv> [/min <3> /max <20>]
Example: seqtools --Mirror.From.NT
Help for command ‘–Palindrome.batch.Task’:

Prototype: seqtools.Utilities::Int32 BatchSearchPalindrome(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --Palindrome.batch.Task /in <in.fasta> /out <outDir> [/min <3> /max <20> /num_threads <-1>]
Example: seqtools --Palindrome.batch.Task
Help for command ‘–Palindrome.From.FASTA’:

Prototype: seqtools.Utilities::Int32 SearchPalindromeFasta(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --Palindrome.From.Fasta /nt <nt-sequence.fasta> [/out <out.csv> /min <3> /max <20>]
Example: seqtools --Palindrome.From.FASTA

Parameters information:

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 /nt
Description: Fasta sequence file, and this file should just contains only one sequence.

Example: /nt ""

[/out]
Description:
Example: /out ""

Accepted Types

/nt

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken
Example:

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{
"Extension": {
"DynamicHash": {
"Properties": [

],
"source": [

]
}
},
"SequenceData": "System.String",
"Attributes": [
"System.String"
]
}

/out

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci
Example:

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{
"Loci": "System.String",
"MirrorSite": "System.String",
"PalEnd": 0,
"Palindrome": "System.String",
"Start": 0
}

Help for command ‘–Palindrome.From.NT’:

Prototype: seqtools.Utilities::Int32 SearchPalindromeNT(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  This function is just for debugger test, /nt parameter is the nucleotide sequence data as ATGCCCC
Usage: G:\GCModeller\manual\bin\seqtools.exe --Palindrome.From.NT /nt <nt-sequence> /out <out.csv> [/min <3> /max <20>]
Example: seqtools --Palindrome.From.NT
Help for command ‘–Palindrome.Imperfects’:

Prototype: seqtools.Utilities::Int32 ImperfectPalindrome(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --Palindrome.Imperfects /in <in.fasta> [/out <out.csv> /min <3> /max <20> /cutoff <0.6> /max-dist <1000 (bp)> /partitions <-1>]
Example: seqtools --Palindrome.Imperfects
Help for command ‘-pattern_search’:

Prototype: seqtools.Utilities::Int32 PatternSearchA(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Parsing the sequence segment from the sequence source using regular expression.
Usage: G:\GCModeller\manual\bin\seqtools.exe -pattern_search -i <file_name> -p <regex_pattern>[ -o <output_directory> -f <format:fsa/gbk>]
Example: seqtools -pattern_search -pattern_search -i ~/xcc8004.txt -p TTA{3}N{1,2} -f fsa

Parameters information:

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    -i
Description: The sequence input data source file, it can be a fasta or genbank file.

Example: -i "~/Desktop/xcc8004.txt"

-p
Description: This switch specific the regular expression pattern for search the sequence segment,
for more detail information about the regular expression please read the user manual.

Example: -p "N{1,5}TA"

[-o]
Description: Optional, this switch value specific the output directory for the result data, default is user Desktop folder.

Example: -o "~/Documents/"

[-f]
Description: Optional, specific the input file format for the sequence reader, default value is FASTA sequence file.
fsa - The input sequence data file is a FASTA format file;
gbk - The input sequence data file is a NCBI genbank flat file.

Example: -f "fsa"

Accepted Types

-i
-p
-o
-f
Help for command ‘–PerfectPalindrome.Filtering’:

Prototype: seqtools.Utilities::Int32 FilterPerfectPalindrome(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --PerfectPalindrome.Filtering /in <inDIR> [/min <8> /out <outDIR>]
Example: seqtools --PerfectPalindrome.Filtering
Help for command ‘Repeats.Density’:

Prototype: seqtools.Utilities::Int32 RepeatsDensity(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe Repeats.Density /dir <dir> /size <size> /ref <refName> [/out <out.csv> /cutoff <default:=0>]
Example: seqtools Repeats.Density
Help for command ‘-reverse’:

Prototype: seqtools.Utilities::Int32 Reverse(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe -reverse -i <input_fasta> [-o <output_fasta>]
Example: seqtools -reverse
Help for command ‘rev-Repeats.Density’:

Prototype: seqtools.Utilities::Int32 revRepeatsDensity(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe rev-Repeats.Density /dir <dir> /size <size> /ref <refName> [/out <out.csv> /cutoff <default:=0>]
Example: seqtools rev-Repeats.Density
Help for command ‘Search.Batch’:

Prototype: seqtools.Utilities::Int32 BatchSearch(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Batch search for repeats.
Usage: G:\GCModeller\manual\bin\seqtools.exe Search.Batch /aln <alignment.fasta> [/min 3 /max 20 /min-rep 2 /out <./>]
Example: seqtools Search.Batch

Parameters information:

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/aln
Description: The input fasta file should be the output of the clustal multiple alignment fasta output.

Example: /aln ""

Accepted Types

/aln
Help for command ‘-segment’:

Prototype: seqtools.Utilities::Int32 GetSegment(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe -segment /fasta <Fasta_Token> [-loci <loci>] [/left <left> /length <length> /right <right> [/reverse]] [/ptt <ptt> /geneID <gene_id> /dist <distance> /downstream] -o <saved> [-line.break 100]
Example: seqtools -segment
Help for command ‘–segments’:

Prototype: seqtools.Utilities::Int32 GetSegments(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --segments /regions <regions.csv> /fasta <nt.fasta> [/complement /reversed /brief-dump]
Example: seqtools --segments

Parameters information:

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    [/reversed]
Description: If the sequence is on the complement strand, reversed it after complement operation?

Example: /reversed ""

[/complement]
Description: If this Boolean switch is set on, then all of the reversed strand segment will be complemenet and reversed.

Example: /complement ""

[/brief-dump]
Description: If this parameter is set up true, then only the locus_tag of the ORF gene will be dump to the fasta sequence.

Example: /brief-dump ""

Accepted Types

/reversed
/complement
/brief-dump
Help for command ‘–ToVector’:

Prototype: seqtools.Utilities::Int32 ToVector(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --ToVector /in <in.DIR> /min <4> /max <8> /out <out.txt> /size <genome.size>
Example: seqtools --ToVector
Help for command ‘–translates’:

Prototype: seqtools.Utilities::Int32 Translates(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Translates the ORF gene as protein sequence. If any error was output from the console, please using > operator dump the output to a log file for the analysis.
Usage: G:\GCModeller\manual\bin\seqtools.exe --translates /orf <orf.fasta> [/transl_table 1 /force]
Example: seqtools --translates

Parameters information:

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 /orf
Description: ORF gene nt sequence should be completely complement and reversed as forwards strand if it is complement strand.

Example: /orf ""

[/force]
Description: This force parameter will force the translation program ignore of the stop code and continute sequence translation.

Example: /force ""

[/transl_table]
Description: Available index value was described at http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes#SG25

Example: /transl_table ""

Accepted Types

/orf
/force
/transl_table
Help for command ‘–Trim’:

Prototype: seqtools.Utilities::Int32 Trim(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\seqtools.exe --Trim /in <in.fasta> [/case <u/l> /break <-1/int> /out <out.fasta> /brief]
Example: seqtools --Trim

Parameters information:

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    [/case]
Description: Adjust the letter case of your sequence, l for lower case and u for upper case. Default value is upper case.

Example: /case ""

[/break]
Description: Adjust the sequence break when this program write the fasta sequence, default is -1 which means no break, write all sequence in one line.

Example: /break ""

Accepted Types

/case
/break