1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
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3 <runnerClassName>compbio.runner.msa.Muscle</runnerClassName>
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6 <name>Protein alignment(Fastest speed)</name>
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8 Fastest possible speed for protein sequences. Gives acceptable quality
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9 alignments for closely related sequences
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12 <option>-maxiters 1</option>
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13 <option>-diags</option>
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14 <option>-sv</option>
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15 <option>-distance1 kbit20_3</option>
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20 <name>Nucleotide alignment(Fastest speed)</name>
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22 Fastest possible speed for nucleotide sequences. Gives acceptable quality
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23 alignments for closely related sequences
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26 <option>-maxiters 1</option>
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27 <option>-diags</option>
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32 <name>Large alignments (balanced)</name>
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34 A large number of sequences (a few thousand), or very long sequences, then the default
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35 settings of may be too slow for practical use. A good compromise between speed and
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36 accuracy is to run just the first two iterations of the algorithm.
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39 <option>-maxiters 2</option>
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