dundee-conf/settings/TcoffeePresets.xml

   1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
   2 <presets>\r
   3         <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
   4         <preset>\r
   5                 <name>Quick align. Very fast approximate (Speed-oriented)</name>\r
   6                 <description>quickaln: Very fast, sequence type - all, accuracy - medium low</description>\r
   7                 <optlist>\r
   8                         <option>-mode quickaln</option>\r
   9                 </optlist>\r
  10         </preset>\r
  11         <!-- does not work\r
  12         <preset>\r
  13                 <name>Dali (Speed-oriented)</name>\r
  14                 <description>dali: a mode used to combine dali pairwise alignments</description>\r
  15                 <optlist>\r
  16                         <option>-mode dali</option>\r
  17                 </optlist>\r
  18         </preset>\r
  19         -->\r
  20         <!-- This requires Blast to operate, however i do not know how to plug it to t-coffee. \r
  21         The build in one does not work.  \r
  22         <preset>\r
  23                 <name>3dcoffee (Accuracy-oriented)</name>\r
  24                 <description>3dcoffee: runs t_coffee with the 3dcoffee  parameterization</description>\r
  25                 <optlist>\r
  26                         <option>-mode 3dcoffee</option>\r
  27                 </optlist>\r
  28         </preset>\r
  29         <preset>\r
  30                 <name>Accurate (Accuracy-oriented)</name>\r
  31                 <description>accurate: slow, sequence type - protein, accuracy - high</description>\r
  32                 <optlist>\r
  33                         <option>-mode accurate</option>\r
  34                 </optlist>\r
  35         </preset>\r
  36         could not find templates(?)\r
  37         <preset>\r
  38                 <name>Rcoffee for RNA only (accuracy-oriented)</name>\r
  39                 <description> rcoffee: slow, sequence type - RNA, accuracy - high</description>\r
  40                 <optlist>\r
  41                         <option>-mode rcoffee</option>\r
  42                 </optlist>\r
  43         </preset>\r
  44          -->\r
  45          <!-- This needs blast\r
  46         <preset>\r
  47                 <name>Expresso (accuracy-oriented)</name>\r
  48                 <description> expresso: slow, sequence type - all, accuracy - high</description>\r
  49                 <optlist>\r
  50                         <option>-mode expresso</option>\r
  51                 </optlist>\r
  52         </preset>\r
  53          --> \r
  54 </presets>\r