1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
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3 <runnerClassName>compbio.runner.msa.MSAprobs</runnerClassName>
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5 <options isRequired="true">
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6 <name>CLUSTAL format for output alignment</name>
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8 CLUSTAL output format is used instead of the FASTA format
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10 <optionNames>-clustalw</optionNames>
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11 <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>
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14 <options isRequired="true">
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15 <name>Another order of sequence in output alignment</name>
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17 print sequences in alignment order rather than input order
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19 <optionNames>-a</optionNames>
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20 <optionNames>--alignment-order</optionNames>
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21 <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>
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24 <prmSeparator> </prmSeparator>
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26 <parameters isRequired="false">
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27 <name>passes of consistency transformation</name>
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29 passes of consistency transformation
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31 <optionNames>-c</optionNames>
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32 <optionNames>--consistency</optionNames>
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33 <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>
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34 <defaultValue>2</defaultValue>
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36 <type>Integer</type>
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42 <parameters isRequired="false">
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43 <name>passes of consistency transformation</name>
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45 number of passes of iterative-refinement
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47 <optionNames>-ir</optionNames>
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48 <optionNames>--iterative-refinement</optionNames>
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49 <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>
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50 <defaultValue>10</defaultValue>
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52 <type>Integer</type>
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58 <parameters isRequired="false">
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59 <name>Number of CPUs</name>
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61 Number of CPU used by msaprobs.
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62 My default the number is equal to the total number of CPU on the system.
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64 <optionNames>-num_threads</optionNames>
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65 <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>
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66 <defaultValue>1</defaultValue>
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68 <type>Integer</type>
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