1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
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3 <runnerClassName>compbio.runner.tcoffee.tcoffee</runnerClassName>
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5 <name>Quick align. Very fast approximate (Speed-oriented)</name>
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6 <description>quickaln: Very fast, sequence type - all, accuracy - medium low</description>
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8 <option>-mode quickaln</option>
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11 <!-- These presets require BLAST and PDB database to be installed correctly neither of these works
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14 <name>Dali (Speed-oriented)</name>
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15 <description>dali: a mode used to combine dali pairwise alignments</description>
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17 <option>-mode dali</option>
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21 <!-- This requires Blast to operate, however i do not know how to plug it to t-coffee.
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22 The build in one does not work.
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24 <name>3dcoffee (Accuracy-oriented)</name>
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25 <description>3dcoffee: runs t_coffee with the 3dcoffee parameterization</description>
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27 <option>-mode 3dcoffee</option>
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31 <name>Accurate (Accuracy-oriented)</name>
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32 <description>accurate: slow, sequence type - protein, accuracy - high</description>
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34 <option>-mode accurate</option>
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40 <name>Rcoffee for RNA only (accuracy-oriented)</name>
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41 <description> rcoffee: slow, sequence type - RNA, accuracy - high</description>
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43 <option>-mode rcoffee</option>
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48 <name>Expresso (accuracy-oriented)</name>
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49 <description> expresso: slow, sequence type - all, accuracy - high</description>
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51 <option>-mode expresso</option>
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