1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
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3 <runnerClassName>compbio.runner.mafft.Mafft</runnerClassName>
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5 <name>L-INS-i (Accuracy-oriented)</name>
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6 <description>L-INS-i (probably most accurate; recommended for <200
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7 sequences; iterative refinement method incorporating local pairwise
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8 alignment information)</description>
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10 <option>--localpair</option>
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11 <option>--maxiterate 1000</option>
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15 <name>G-INS-i (Accuracy-oriented)</name>
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16 <description>G-INS-i (suitable for sequences of similar lengths;
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17 recommended for <200 sequences; iterative refinement method
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18 incorporating global pairwise alignment information)</description>
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20 <option>--globalpair</option>
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21 <option>--maxiterate 1000</option>
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25 <name>E-INS-i (Accuracy-oriented)</name>
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26 <description>E-INS-i (suitable for sequences containing large
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27 unalignable regions; recommended for <200 sequences)</description>
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29 <option>--ep 0</option>
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30 <option>--genafpair</option>
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31 <option>--maxiterate 1000</option>
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35 <name>FFT-NS-i (Speed oriented)</name>
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36 <description>FFT-NS-i (iterative refinement method; two cycles only)</description>
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38 <option>--retree 2</option>
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39 <option>--maxiterate 2</option>
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43 <name>FFT-NS-1 (Speed oriented)</name>
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44 <description>FFT-NS-1 (very fast; recommended for >2000 sequences;
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45 progressive method with a rough guide tree)</description>
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47 <option>--retree 1</option>
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48 <option>--maxiterate 0</option>
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52 <name>NW-NS-PartTree-1 (Speed oriented)</name>
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53 <description>NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000
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54 sequences; progressive method with the PartTree algorithm)</description>
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56 <option>--retree 1</option>
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57 <option>--maxiterate 0</option>
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58 <option>--nofft</option>
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59 <option>--parttree</option>
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