Documentation ¶
Overview ¶
Package muscle implements interaction with the MUSCLE multiple alignment tool. MUSCLE is available from http://www.drive5.com/muscle/
Index ¶
Constants ¶
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Variables ¶
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Functions ¶
This section is empty.
Types ¶
type Muscle ¶
type Muscle struct { // Usage: muscle -in <inputfile> -out <outputfile> // // Common options (for a complete list please see the User Guide): // // -in <inputfile> Input file in FASTA format (default stdin) // -out <outputfile> Output alignment in FASTA format (default stdout) // -diags Find diagonals (faster for similar sequences) // -maxiters <n> Maximum number of iterations (integer, default 16) // -maxhours <h> Maximum time to iterate in hours (default no limit) // -html Write output in HTML format (default FASTA) // -msf Write output in GCG MSF format (default FASTA) // -clw Write output in CLUSTALW format (default FASTA) // -clwstrict As -clw, with 'CLUSTAL W (1.81)' header // -log[a] <logfile> Log to file (append if -loga, overwrite if -log) // -quiet Do not write progress messages to stderr // -version Display version information and exit // // Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2 // Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3 // Fastest possible (nucleotides): -maxiters 1 -diags Cmd string `buildarg:"{{if .}}{{.}}{{else}}muscle{{end}}"` // muscle // Files: InFile string `buildarg:"{{if .}}-in{{split}}{{.}}{{end}}"` // -in <inputfile> OutFile string `buildarg:"{{if .}}-out{{split}}{{.}}{{end}}"` // -out <outputfile> Log Log `buildarg:"{{if .File}}-log{{if .Append}}a{{end}}{{split}}{{.File}}{{end}}"` // -log[a] <logfile> Quiet bool `buildarg:"{{if .}}-quiet{{end}}"` // -quiet // Formatting: Html bool `buildarg:"{{if .}}-html{{end}}"` // -html Msf bool `buildarg:"{{if .}}-msf{{end}}"` // -msf Clustal bool `buildarg:"{{if .}}-clw{{end}}"` // -clw ClustalStrict bool `buildarg:"{{if .}}-clwstrict{{end}}"` // -clwstrict // Common options: FindDiagonals bool `buildarg:"{{if .}}-diags{{end}}"` // -diags MaxIterations int `buildarg:"{{if .}}-maxiters{{split}}{{.}}{{end}}"` // -maxiters <n> MaxDuration time.Duration `buildarg:"{{if .}}-maxhours{{split}}{{hours .}}{{end}}"` // -maxhours <h> // Other value options (see MUSCLE user guide): // Gleaned from user guide - may not reflect reality. AnchorSpacing int `buildarg:"{{if .}}-anchorspacing{{split}}{{.}}{{end}}"` // -anchorspacing <n> Center float64 `buildarg:"{{if .}}-center{{split}}{{.}}{{end}}"` // -center <f.> Cluster1 string `buildarg:"{{if .}}-cluster1{{split}}{{.}}{{end}}"` // -cluster1 "upgma|upgma|neighborjoining" Cluster2 string `buildarg:"{{if .}}-cluster2{{split}}{{.}}{{end}}"` // -cluster2 "upgma|upgma|neighborjoining" ClustalOut string `buildarg:"{{if .}}-clwout{{split}}{{.}}{{end}}"` // -clwout <file> DiagonalBreak int `buildarg:"{{if .}}-diagbreak{{split}}{{.}}{{end}}"` // -diagbreak <n> DiagonalLength int `buildarg:"{{if .}}-diaglength{{split}}{{.}}{{end}}"` // -diaglength <n> DiagonalMargin int `buildarg:"{{if .}}-diagmargin{{split}}{{.}}{{end}}"` // -diagmargin <n> Distance1 string `buildarg:"{{if .}}-distance1{{split}}{{.}}{{end}}"` // -distance1 "kmer6_6|kmer20_3|kmer20_4|kbit20_3|kmer4_6" Distance2 string `buildarg:"{{if .}}-distance2{{split}}{{.}}{{end}}"` // -distance2 "pctid_kimura|pctid_log" FastaOut string `buildarg:"{{if .}}-fastaout{{split}}{{.}}{{end}}"` // -fastaout <file> GapOpen float64 `buildarg:"{{if .}}-gapopen{{split}}{{.}}{{end}}"` // -gapopen <f.> GapExtend float64 `buildarg:"{{if .}}-gapextend{{split}}{{.}}{{end}}"` // -gapextend <f.> HydroWindow int `buildarg:"{{if .}}-hydro{{split}}{{.}}{{end}}"` // -hydro <n> HydroFactor float64 `buildarg:"{{if .}}-hydrofactor{{split}}{{.}}{{end}}"` // -hydrofactor <f.> In1 string `buildarg:"{{if .}}-in1{{split}}{{.}}{{end}}"` // -in1 <file> In2 string `buildarg:"{{if .}}-in2{{split}}{{.}}{{end}}"` // -in2 <file> Matrix string `buildarg:"{{if .}}-matrix{{split}}{{.}}{{end}}"` // -matrix <file> MaxTrees int `buildarg:"{{if .}}-maxtrees{{split}}{{.}}{{end}}"` // -maxtrees <n> MinBestColScore float64 `buildarg:"{{if .}}-minbestcolscore{{split}}{{.}}{{end}}"` // -minbestcolscore <f.> MinSmoothScore float64 `buildarg:"{{if .}}-minsmoothscore{{split}}{{.}}{{end}}"` // -minsmoothscore <f.> MsaOut string `buildarg:"{{if .}}-msaout{{split}}{{.}}{{end}}"` // -msaout <file> ObjectiveScore string `buildarg:"{{if .}}-objscore{{split}}{{.}}{{end}}"` // -objscore "sp|ps|dp|xp|spf|spm" PhyInterOut string `buildarg:"{{if .}}-phyiout{{split}}{{.}}{{end}}"` // -phyiout <file> PhySequenOut string `buildarg:"{{if .}}-physout{{split}}{{.}}{{end}}"` // -physout <file> RefineWindow int `buildarg:"{{if .}}-refinewindow{{split}}{{.}}{{end}}"` // -refinewindow <n> Root1 string `buildarg:"{{if .}}-root1{{split}}{{.}}{{end}}"` // -root1 "pseudo|midlongestspan|minavgleafdist" Root2 string `buildarg:"{{if .}}-root2{{split}}{{.}}{{end}}"` // -root2 "pseudo|midlongestspan|minavgleafdist" ScoreFile string `buildarg:"{{if .}}-scorefile{{split}}{{.}}{{end}}"` // -scorefile <file> SeqType string `buildarg:"{{if .}}-seqtype{{split}}{{.}}{{end}}"` // -seqtype "protein|nucleo|auto" SmoothScoreCeil float64 `buildarg:"{{if .}}-smoothscoreceil{{split}}{{.}}{{end}}"` // -smoothscoreceil <f.> SmoothWindow int `buildarg:"{{if .}}-smoothwindow{{split}}{{.}}{{end}}"` // -smoothwindow <n> SpScore string `buildarg:"{{if .}}-spscore{{split}}{{.}}{{end}}"` // -spscore <file> Tree1 string `buildarg:"{{if .}}-tree1{{split}}{{.}}{{end}}"` // -tree1 <file> Tree2 string `buildarg:"{{if .}}-tree2{{split}}{{.}}{{end}}"` // -tree2 <file> UseTree string `buildarg:"{{if .}}-usetree{{split}}{{.}}{{end}}"` // -usetree <file> Weight1 string `buildarg:"{{if .}}-weight1{{split}}{{.}}{{end}}"` // -weight1 "none|henikoff|henikoffpb|gsc|clustalw|threeway" Weight2 string `buildarg:"{{if .}}-weight2{{split}}{{.}}{{end}}"` // -weight2 "none|henikoff|henikoffpb|gsc|clustalw|threeway" // Other flag options (see MUSCLE user guide): // Gleaned from user guide - may not reflect reality. Anchors bool `buildarg:"{{if .}}-anchors{{end}}"` // -anchors Brenner bool `buildarg:"{{if .}}-brenner{{end}}"` // -brenner Cluster bool `buildarg:"{{if .}}-cluster{{end}}"` // -cluster Dimer bool `buildarg:"{{if .}}-dimer{{end}}"` // -dimer Core bool `buildarg:"{{if .}}-core{{end}}"` // -core Diags1 bool `buildarg:"{{if .}}-diags1{{end}}"` // -diags1 Diags2 bool `buildarg:"{{if .}}-diags2{{end}}"` // -diags2 Fasta bool `buildarg:"{{if .}}-fasta{{end}}"` // -fasta Group bool `buildarg:"{{if .}}-group{{end}}"` // -group LogExpectation bool `buildarg:"{{if .}}-le{{end}}"` // -le NoAnchors bool `buildarg:"{{if .}}-noanchors{{end}}"` // -noanchors NoCore bool `buildarg:"{{if .}}-nocore{{end}}"` // -nocore PhylipInter bool `buildarg:"{{if .}}-phyi{{end}}"` // -phyi PhylipSequen bool `buildarg:"{{if .}}-phys{{end}}"` // -phys Profile bool `buildarg:"{{if .}}-profile{{end}}"` // -profile Refine bool `buildarg:"{{if .}}-refine{{end}}"` // -refine RefineByWindow bool `buildarg:"{{if .}}-refinew{{end}}"` // -refinew SumOfPairsProt bool `buildarg:"{{if .}}-sp{{end}}"` // -sp PPScore bool `buildarg:"{{if .}}-ppscore{{end}}"` // -ppscore SumOfPairsNuc bool `buildarg:"{{if .}}-spn{{end}}"` // -spn SumOfPairsProf bool `buildarg:"{{if .}}-sv{{end}}"` // -sv Verbose bool `buildarg:"{{if .}}-verbose{{end}}"` // -verbose }
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