updates to jaba2 from jaba release branch

[jabaws.git] / dundee-conf / settings / TcoffeePresets.xml

diff --git a/dundee-conf/settings/TcoffeePresets.xml b/dundee-conf/settings/TcoffeePresets.xml
new file mode 100644 (file)
index 0000000..585bb21
--- /dev/null
+++ b/dundee-conf/settings/TcoffeePresets.xml
@@ -0,0 +1,54 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<presets>\r
+       <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
+       <preset>\r
+               <name>Quick align. Very fast approximate (Speed-oriented)</name>\r
+               <description>quickaln: Very fast, sequence type - all, accuracy - medium low</description>\r
+               <optlist>\r
+                       <option>-mode quickaln</option>\r
+               </optlist>\r
+       </preset>\r
+       <!-- does not work\r
+       <preset>\r
+               <name>Dali (Speed-oriented)</name>\r
+               <description>dali: a mode used to combine dali pairwise alignments</description>\r
+               <optlist>\r
+                       <option>-mode dali</option>\r
+               </optlist>\r
+       </preset>\r
+       -->\r
+       <!-- This requires Blast to operate, however i do not know how to plug it to t-coffee. \r
+       The build in one does not work.  \r
+       <preset>\r
+               <name>3dcoffee (Accuracy-oriented)</name>\r
+               <description>3dcoffee: runs t_coffee with the 3dcoffee  parameterization</description>\r
+               <optlist>\r
+                       <option>-mode 3dcoffee</option>\r
+               </optlist>\r
+       </preset>\r
+       <preset>\r
+               <name>Accurate (Accuracy-oriented)</name>\r
+               <description>accurate: slow, sequence type - protein, accuracy - high</description>\r
+               <optlist>\r
+                       <option>-mode accurate</option>\r
+               </optlist>\r
+       </preset>\r
+       could not find templates(?)\r
+       <preset>\r
+               <name>Rcoffee for RNA only (accuracy-oriented)</name>\r
+               <description> rcoffee: slow, sequence type - RNA, accuracy - high</description>\r
+               <optlist>\r
+                       <option>-mode rcoffee</option>\r
+               </optlist>\r
+       </preset>\r
+        -->\r
+        <!-- This needs blast\r
+       <preset>\r
+               <name>Expresso (accuracy-oriented)</name>\r
+               <description> expresso: slow, sequence type - all, accuracy - high</description>\r
+               <optlist>\r
+                       <option>-mode expresso</option>\r
+               </optlist>\r
+       </preset>\r
+        --> \r
+</presets>\r