1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
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3 <runnerClassName>compbio.runner.msa.ClustalO</runnerClassName>
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7 <description>Dealign input sequences</description>
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8 <optionNames>--dealign</optionNames>
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9 <furtherDetails>prog_docs/clustalo.txt</furtherDetails>
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13 <name>Full distance matrix</name>
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14 <description>Use full distance matrix for guide-tree calculation (slow; mBed is default)</description>
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15 <optionNames>--full</optionNames>
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16 <furtherDetails>prog_docs/clustalo.txt</furtherDetails>
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20 <name>Full distance matrix for each iteration</name>
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21 <description>Use full distance matrix for guide-tree calculation during iteration (mBed is default)</description>
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22 <optionNames>--full-iter</optionNames>
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23 <furtherDetails>prog_docs/clustalo.txt</furtherDetails>
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26 <prmSeparator>=</prmSeparator>
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29 <name>Max Guide tree iterations</name>
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30 <description>Maximum number of HMM iterations</description>
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31 <optionNames>--max-hmm-iterations</optionNames>
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32 <furtherDetails>prog_docs/clustalo.txt</furtherDetails>
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33 <defaultValue>1</defaultValue>
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35 <type>Integer</type>
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42 <name>Number of iterations (combined)</name>
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43 <description>Number of (combined guide tree/HMM) iterations</description>
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44 <optionNames>--iter</optionNames>
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45 <furtherDetails>prog_docs/clustalo.txt</furtherDetails>
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46 <defaultValue>1</defaultValue>
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48 <type>Integer</type>
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55 <name>Max Guide tree iterations</name>
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56 <description>Maximum guide tree iterations</description>
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57 <optionNames>--max-guidetree-iterations</optionNames>
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58 <furtherDetails>prog_docs/clustalo.txt</furtherDetails>
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59 <defaultValue>1</defaultValue>
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61 <type>Integer</type>
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