MUSCLE
This test reflects how Mucle is run by ViPR.
It should be used any time changes are made to the Muscle interface.

runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
infile_ - Primary Input File
data_type_ - Excl - Data type (-seqtype)
stable_ - Switch - Preserve the order of the input sequences
make_scorefile_ - Switch - Write a Matrix Score File
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clusteronly_para
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clusteronly_ - Switch - Use clustering only (upgma)
clusteronlymaxiters_ - Integer - Number of iterations for Clustering (-maxiters)
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runparams
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maxiterations_ - Integer - Number of iterations (-maxiters)
max_mem_ - Integer - Set the Maximum Memory to be allocated for this job
protprofilefunction_ - Excl - Specify Protein Profile Scoring Function
hydrowindow_ - Integer - Window size for determining whether a region is hydrophobic. Protein only. (-hydro)
hydrofactormultiplier_ - Float - Multiplier for gap open/close penalties in hydrophobic regions, protein only (-hydrofactor)
logfile_ - Switch - Produce a logfile containing the command line? (-log)
verboselogfile_ - Switch - Produce a more verbose logfile? (-verbose)
logfileout_ - Results -
verboselogfileout_ - Results -
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User_matrix
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add_matrix_ - Switch - User Supplied Matrix
mymatrix_ - InFile - Matrix File (NCBI or WU-BLAST format)
gpopen_ - Float - Gap Open Penalty (must be negative)
gpextend_ - Float - Gap Extend Penalty (must be negative)
ctr_ - Float - Center Value (must be zero or negative)
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Diagonal_Options
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use_diags_ - Switch - Use Diagonals
diagfunction_ - List - Diagonal Functions (-diags)
maxdiagdist_ - Integer - Maximum distance between two diagonals that allows them to merge into one diagonal. (-diagbreak)
mindiaglength_ - Integer - Minimum length of diagonal (-diaglength)
diagmarginpos_ - Integer - Discard this many positions at ends of diagonal (-diagmargin)
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tree_options
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use_guide_tree_ - Switch - Provide a Guide Tree
guidetree_ - InFile - Guide Tree File; Newick/Phylip format (-usetree)
make_tree1file_ - Switch - Save tree produced in first iteration in Newick (Phylip-compatible) format
make_tree2file_ - Switch - Save tree produced in second iteration in Newick (Phylip-compatible) format
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options1
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use_weights_1_ - Switch - Use Weights for Iterations 1 and 2
weight1_ - Excl - Sequence weighting scheme for Iteration 1: (-weight1)
distance1p_ - Excl - Distance measure for iteration 1; Protein only (-distance1)
cluster1_ - Excl - Clustering for Iterations 1 and 2: (-cluster1)
sueff1_ - Float - SUEFF(must be between 0 and 1)
root1_ - Excl - Method used to root tree in iterations 1 and 2 (-root1)
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options2
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maxtrees_ - Integer - Maximum trees in Iteration 2 (-maxtrees)
use_weights_2_ - Switch - Use Weights for Iterations 3 and beyond
weight2_ - Excl - Sequence weighting for tree-dependent refinement.
distance2_ - Excl - Distance Measure for Iterations 2 and above (-distance2)
cluster2_ - Excl - Clustering method for later iterations: (-cluster2)
sueff2_ - Float - SUEFF(must be between 0 and 1)
root2_ - Excl - Method used to root tree in iterations 3 and beyond (-root2)
objectivescore_ - Excl - Objective score used by tree dependent refinement (-objscore)
anchor_ - Switch - Use Anchor Optimization (-noanchors) This option has no effect if -maxiters 1 or -maxiters 2 is specified.
minanchorcolumnspacing_ - Integer - Minimum spacing between anchor columns
minanchorcolumnscore_ - Float - Minimum score a column must have to be an anchor
minsmoothanchorscore_ - Float - Minimum smoothed score a column must have to be an anchor
anchorsmoothingwindow_ - Integer - Window Used for Anchor Smoothing
Section: ****************************************************************************
output_options
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output_fasta_ - Switch - Fasta output
output_clustal_ - Switch - Clustal output (.aln)
output_clustals_ - Switch -
Strict Clustal output (.aln; has the Clustal header)
output_html_ - Switch - HTML output (.html)
output_gcg_ - Switch - GCG output (.msf)
output_phyi_ - Switch - Interleaved Phylip output
output_phys_ - Switch -
Sequential Phylip output (.phy)