testsrc/testdata/MusclePresets.xml

   1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
   2 <presets>\r
   3         <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
   4         <preset>\r
   5                 <name>Protein alignment(Fastest speed)</name>\r
   6                 <description>Fastest possible speed for protein sequences. Gives acceptable quality alignments for closely related sequences</description>\r
   7                 <optlist>\r
   8                         <option>-maxiters 1</option>\r
   9                         <option>-diags</option>\r
  10                         <option>-sv</option>\r
  11                         <option>-distance1 kbit20_3</option>\r
  12                 </optlist>\r
  13         </preset>\r
  14         <preset>\r
  15                 <name>Nucleotide alignment(Fastest speed)</name>\r
  16                 <description>Fastest possible speed for nucleotide sequences. Gives acceptable quality alignments for closely related sequences</description>\r
  17                 <optlist>\r
  18                         <option>-maxiters 1</option>\r
  19                         <option>-diags</option>\r
  20                 </optlist>\r
  21         </preset>\r
  22         <preset>\r
  23                 <name>Large alignments (balanced)</name>\r
  24                 <description>A large number of sequences (a few thousand), or very long sequences, \r
  25                 then the default settings of may be too slow for practical use. \r
  26                 A good compromise between speed and accuracy is to run just the first two iterations of \r
  27                 the algorithm</description>\r
  28                 <optlist>\r
  29                         <option>-maxiters 2</option>\r
  30                 </optlist>\r
  31         </preset>\r
  32 </presets>\r