1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
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3 <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>
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5 <name>Protein alignment(Fastest speed)</name>
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6 <description>Fastest possible speed for protein sequences. Gives acceptable quality alignments for closely related sequences</description>
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8 <option>-maxiters 1</option>
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9 <option>-diags</option>
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10 <option>-sv</option>
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11 <option>-distance1 kbit20_3</option>
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15 <name>Nucleotide alignment(Fastest speed)</name>
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16 <description>Fastest possible speed for nucleotide sequences. Gives acceptable quality alignments for closely related sequences</description>
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18 <option>-maxiters 1</option>
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19 <option>-diags</option>
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23 <name>Huge alignments (speed-oriented)</name>
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24 <description>Very large number of sequences (several thousand), or they are very long, </description>
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26 <option>-maxiters 1</option>
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27 <option>-diags1</option>
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28 <option>-sv</option>
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