1 MUSCLE v3.7 by Robert C. Edgar
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3 http://www.drive5.com/muscle
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4 This software is donated to the public domain.
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5 Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
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10 muscle -in <inputfile> -out <outputfile>
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12 Common options (for a complete list please see the User Guide):
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14 -in <inputfile> Input file in FASTA format (default stdin)
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15 -out <outputfile> Output alignment in FASTA format (default stdout)
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16 -diags Find diagonals (faster for similar sequences)
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17 -maxiters <n> Maximum number of iterations (integer, default 16)
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18 -maxhours <h> Maximum time to iterate in hours (default no limit)
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19 -maxmb <m> Maximum memory to allocate in Mb (default 80% of RAM)
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20 -html Write output in HTML format (default FASTA)
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21 -msf Write output in GCG MSF format (default FASTA)
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22 -clw Write output in CLUSTALW format (default FASTA)
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23 -clwstrict As -clw, with 'CLUSTAL W (1.81)' header
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24 -log[a] <logfile> Log to file (append if -loga, overwrite if -log)
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25 -quiet Do not write progress messages to stderr
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26 -stable Output sequences in input order (default is -group)
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27 -group Group sequences by similarity (this is the default)
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28 -version Display version information and exit
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30 Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2
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31 Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3
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32 Fastest possible (nucleotides): -maxiters 1 -diags
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