updates to jaba2 from jaba release branch

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

diff --git a/dundee-conf/settings/MusclePresets.xml b/dundee-conf/settings/MusclePresets.xml
new file mode 100644 (file)
index 0000000..190adad
--- /dev/null
+++ b/dundee-conf/settings/MusclePresets.xml
@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<presets>\r
+       <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
+       <preset>\r
+               <name>Protein alignment(Fastest speed)</name>\r
+               <description>Fastest possible speed for protein sequences. Gives acceptable quality alignments for closely related sequences</description>\r
+               <optlist>\r
+                       <option>-maxiters 1</option>\r
+                       <option>-diags</option>\r
+                       <option>-sv</option>\r
+                       <option>-distance1 kbit20_3</option>\r
+               </optlist>\r
+       </preset>\r
+       <preset>\r
+               <name>Nucleotide alignment(Fastest speed)</name>\r
+               <description>Fastest possible speed for nucleotide sequences. Gives acceptable quality alignments for closely related sequences</description>\r
+               <optlist>\r
+                       <option>-maxiters 1</option>\r
+                       <option>-diags</option>\r
+               </optlist>\r
+       </preset>\r
+       <preset>\r
+               <name>Huge alignments (speed-oriented)</name>\r
+               <description>Very large number of sequences (several thousand), or they are very long, </description>\r
+               <optlist>\r
+                       <option>-maxiters 1</option>\r
+                       <option>-diags1</option>\r
+                       <option>-sv</option>\r
+               </optlist>\r
+       </preset>\r
+</presets>\r