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
deleted file mode 100644 (file)
index 190adad..0000000
--- a/dundee-conf/settings/MusclePresets.xml
+++ /dev/null
@@ -1,31 +0,0 @@
-<?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