Get 1000 Hours free
On the UCSD Supercomputer
Start Your TrialThe tool id for this interface is clustalw. It is selected with tool=clustalw
Supported parameters for tool=clustalw that require input files are:
input.infile_ - InFile - Primary Input File
input.usetreee_ - InFile - Guide Tree (-usetree)
input.profile1_ - InFile - Profile 1 (-profile1)
input.profile2_ - InFile - Profile 2 (-profile2)
input.usetreee1_ - InFile - Guide Tree for profile 1 (-usetree1)
input.usetreee2_ - InFile - Guide Tree for profile 1 (-usetree2)
input.exclude_file_ - InFile - Choose an input file that excludes the range of positions specifed in this file (-E)
input.constraint_ - InFile - Constraint (-g).
Other supported parameters for tool=clustalw are:
vparam.runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly) default=0.25, max = 168
vparam.phylip_alig_ - Switch - Phylip alignment output format (-output) default = 0.
vparam.quicktree_ - Excl - Toggle Slow/Fast pairwise alignments (-quicktree); slow or fast; default=slow
vparam.actions_ - Excl - Actions - default: -align, also: -profile, -sequences, -tree, -bootstrap
Multiple Alignment Parameters:
vparam.typeseq_ - Excl - protein or dna (-type) default=dna
vparam.matrix_ - Excl - Protein weight matrix (-matrix) gonnet, blosum, pam, id, default=gonnet
vparam.dnamatrix_ - Excl - DNA weight matrix (-dnamatrix) iub, clustalw default=iub
vparam.gapopen_ - Integer - Gap opening penalty (-gapopen) default=10
vparam.gapext_ - Float - Gap extension penalty (-gapext) default=0.2
vparam.endgaps_ - Switch - End gap separation penalty (-endgaps) default=1
vparam.gapdist_ - Integer - Gap separation pen. range (-gapdist) default=8
vparam.pgap_ - Switch - Residue specific penalties (Pascarella gaps) (-nopgap) default=1
vparam.hgap_ - Switch - Hydrophilic gaps (-nohgap) default=1
hgapresidues_ - List - Hydrophilic residues list (-hgapresidues) default: G,P,S,N,D,Q,E,K,R
vparam.maxdiv_ - Integer - Delay divergent sequences : % ident. for delay (-maxdiv) default=30
vparam.negative_ - Switch - Negative values in matrix ? (-negative) default=0
vparam.transweight_ - Float - Transitions weight (between 0 and 1) (-transweight) default=0.5
Fast Pairwise Alignments parameters
vparam.ktuple_ - Integer - Word size (-ktuple) default=1
vparam.topdiags_ - Integer - Number of best diagonals (-topdiags) default=5
vparam.window_ - Integer - Window around best diags (-window) default=5
vparam.pairgap_ - Float - Gap penalty (-pairgap) default=3
vparam.score_ - Excl - Percent or absolute score ? (-score) percent or absolute
Slow Pairwise Alignments parameters
vparam.pwmatrix_ - Excl - Protein weight matrix (-pwmatrix) blosum, gonnet, pam, id default=gonnet
vparam.pwdnamatrix_ - Excl - DNA weight matrix (-pwdnamatrix) iub,clustalw default=iub
vparam.pwgapopen_ - Float - Gap opening penalty (-pwgapopen) default=10
vparam.pwgapext_ - Float - Gap extension penalty (-pwgapext) default=0.10
Tree Parameters
vparam.kimura_ - Switch - Use Kimura's correction (multiple substitutions) ? (-kimura) default=0
vparam.tossgaps_ - Switch - Ignore positions with gaps ? (-tossgaps) default=0
vparam.bootstrap_ - Integer - Bootstrap a NJ tree (give the number of bootstraps, 0 for none) (-bootstrap) default=1000
vparam.bootlabels_ - Excl - Phylip bootstrap positions (-bootlabels) node or branch
vparam.seed_ - Integer - Seed number for bootstraps (-seed) no default
vparam.outputtree_ - Excl - Output tree/distance format (-outputtree) NJ, PHYLIP, DIST, NEXUS
Output Parameters
vparam.output_ - Excl - CLUSTALW, GCG, GDE, PHYLIP, PIR, NEXUS default=CLUSTALW
vparam.gde_lower_ - Switch - Upper case GDE output (-case) 1=upper, 0=lower
vparam.outorder_ - Excl - Result order (-outorder) inpiut or aligned
vparam.seqnos_ - Switch - Output sequence numbers in the output file (clustalw format) (-seqnos) default=0
Structure Alignment Parameters
vparam.nosecstr1_ - Switch - Use profile 1 secondary structure / penalty mask (-nosecstr1) default=1
vparam.nosecstr2_ - Switch - Use profile 2 secondary structure / penalty mask (-nosecstr2) default=1
vparam.helixgap_ - Integer - Helix gap penalty (-helixgap) default=4
vparam.strandgap_ - Integer - Strand gap penalty (-strandgap) default=4
vparam.loopgap_ - Integer - Loop gap penalty (-loopgap) default=1
vparam.terminalgap_ - Integer - Secondary structure terminal penalty (-terminalgap) default=2
vparam.helixendin_ - Integer - Helix terminal positions: number of residues inside helix to be treated as terminal (-helixendin) default=3
vparam.helixendout_ - Integer - Helix terminal positions: number of residues outside helix to be treated as terminal (-helixendout) default=0
vparam.strandendin_ - Integer - Strand terminal positions: number of residues inside strand to be treated as terminal (-strandendin) default=1
vparam.strandendout_ - Integer - Strand terminal positions: number of residues outside strand to be treated as terminal (-strandendout) default=1
vparam.secstrout_ - Excl - Output in alignment (-secstrout) STRUCTURE, MASK, BOTH, NONE default=STRUCTURE
If there is a tool or a feature you need, please let us know>