testsrc/testdata/MafftPresets.xml

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