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Start Your TrialMUSCLE is public domain multiple alignment software for protein and nucleotide sequences. MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation. MUSCLE creates multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that give the best average accuracy in our tests. Using versions current at the time of writing, my tests show that MUSCLE can achieve both better average accuracy and better speed than CLUSTALW or T‑Coffee, depending on the chosen options.
toolId=MUSCLE
input.infile_ - Primary Input File
input.mymatrix_ - InFile - Matrix File (NCBI or WU-BLAST format) (when add_matrix=1)
input.guidetree_ - InFile - Guide Tree File; Newick/Phylip format (-usetree) (use with use_guide_tree)
vparam.runtime_ - Float - Maximum Hours to Run. default=0.5
vparam.data_type_ - Excl - Data type (-seqtype) protein, dna, rna, auto (default)
vparam.stable_ - Switch - Preserve the order of the input sequences (default=0)
vparam.make_scorefile_ - Switch - Write a Matrix Score File (default=0)
vparam.clusteronly_ - Switch - Use clustering only (upgma) (default=0)
vparam.clusteronlymaxiters_ - Integer - Number of iterations for Clustering (clusteronly_ must =1; default=1) (-maxiters)
vparam.maxiterations_ - Integer - Number of iterations (clusteronly_ must =0)(-maxiters) (default=16)
vparam.max_mem_ - Integer - Set the Maximum Memory to be allocated for this job. (default=30000000)
vparam.protprofilefunction_ - Excl - Specify Protein Profile Scoring Function. (-le, -sp, -sv; default=-le)
vparam.hydrowindow_ - Integer - Window size for determining whether a region is hydrophobic. Protein only. (-hydro) (default=5)
vparam.hydrofactormultiplier_ - Float - Multiplier for gap open/close penalties in hydrophobic regions, protein only (-hydrofactor) default=1.2
vparam.logfile_ - Switch - Produce a logfile containing the command line? (-log) default=1
vparam.verboselogfile_ - Switch - Produce a more verbose logfile? (-verbose) default=0
vparam.add_matrix_ - Switch - User Supplied Matrix (default=0)
vparam.gpopen_ - Float - Gap Open Penalty (must be negative) default depend on scoring matrix
vparam.gpextend_ - Float - Gap Extend Penalty (must be negative) default depend on scoring matrix
vparam.ctr_ - Float - Center Value (must be zero or negative) default depend on scoring matrix
vparam.use_diags_ - Switch - Use Diagonals default=0
vparam.diagfunction_ - List - Diagonal Functions (-diags) -diags1, -diags2; -diags (default)
vparam.maxdiagdist_ - Integer - Maximum distance between two diagonals that allows them to merge into one diagonal. (-diagbreak) default=1.
vparam.mindiaglength_ - Integer - Minimum length of diagonal (-diaglength) default=24.
vparam.diagmarginpos_ - Integer - Discard this many positions at ends of diagonal (-diagmargin) default=5.
vparam.use_guide_tree_ - Switch - Provide a Guide Tree (default=0)
vparam.make_tree1file_ - Switch - Save tree produced in first iteration in Newick (Phylip-compatible) format (default=0)
vparam.make_tree2file_ - Switch - Save tree produced in second iteration in Newick (Phylip-compatible) format (default=0)
vparam.use_weights_1_ - Switch - Use Weights for Iterations 1 and 2 (default=0)
vparam.weight1_ - Excl - Sequence weighting scheme for Iteration 1: (-weight1) henikoff; henikoffpb; gsc; clustalw (default); threeway.
vparam.distance1p_ - Excl - Distance measure for iteration 1; Protein only (-distance1) kmer6_6 (default); kmer20_3; kmer20_4; kbit20_3; kmer4_6.
vparam.cluster1_ - Excl - Clustering for Iterations 1 and 2: (-cluster1) upgma; upgmb (default); neighborjoining
vparam.sueff1_ - Float - SUEFF(must be between 0 and 1) default=0.1
vparam.root1_ - Excl - Method used to root tree in iterations 1 and 2 (-root1) pseudo (default); midlongestspan; minavgleafdist
vparam.maxtrees_ - Integer - Maximum trees in Iteration 2 (-maxtrees). default=1
vparam.use_weights_2_ - Switch - Use Weights for Iterations 3 and beyond. default=0
vparam.weight2_ - Excl - Sequence weighting for tree-dependent refinement. henikoff; henikoffpb; gsc; clustalw (default); threeway
vparam.distance2_ - Excl - Distance Measure for Iterations 2 and above (-distance2): kmer20_3; kmer20_4; kbit20_3; pctidkimura (default); pctidlog
vparam.cluster2_ - Excl - Clustering method for later iterations: (-cluster2) upgma; upgmb (default); neighborjoining
vparam.sueff2_ - Float - SUEFF (must be between 0 and 1) default=0.1
vparam.root2_ - Excl - Method used to root tree in iterations 3 and beyond (-root2) pseudo (default); midlongestspan; minavgleafdist
vparam.objectivescore_ - Excl - Objective score used by tree dependent refinement (-objscore) sp (default); spf; spm; ps; dp; xp
vparam.anchor_ - Switch - Use Anchor Optimization (-noanchors) This option has no effect if -maxiters 1 or -maxiters 2 is specified. default=0
vparam.minanchorcolumnspacing_ - Integer - Minimum spacing between anchor columns. default=32
vparam.minanchorcolumnscore_ - Float - Minimum score a column must have to be an anchor. default=1
vparam.minsmoothanchorscore_ - Float - Minimum smoothed score a column must have to be an anchor. default=1
vparam.anchorsmoothingwindow_ - Integer - Window Used for Anchor Smoothing. default=7
vparam.output_fasta_ - Switch - Fasta output default=0
vparam.output_clustal_ - Switch - Clustal output (.aln) default=0
vparam.output_clustals_ - Switch - Strict Clustal output (.aln; has the Clustal header) default=0
vparam.output_html_ - Switch - HTML output (.html) default=0
vparam.output_gcg_ - Switch - GCG output (.msf) default=0
vparam.output_phyi_ - Switch - Interleaved Phylip output default=0
vparam.output_phys_ - Switch - default=0