Merge branch 'JABAWS_Release_2_5' into develop

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

diff --git a/conf/settings/MusclePresets.xml b/conf/settings/MusclePresets.xml
index 6b63ac6..04bcfb7 100644 (file)
--- a/conf/settings/MusclePresets.xml
+++ b/conf/settings/MusclePresets.xml
@@ -1,32 +1,42 @@
 <?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>Large alignments (balanced)</name>\r
-               <description>A large number of sequences (a few thousand), or very long sequences, \r
-               then the default settings of may be too slow for practical use. \r
-               A good compromise between speed and accuracy is to run just the first two iterations of \r
-               the algorithm</description>\r
-               <optlist>\r
-                       <option>-maxiters 2</option>\r
-               </optlist>\r
-       </preset>\r
+    <runnerClassName>compbio.runner.msa.Muscle</runnerClassName>\r
+\r
+    <preset>\r
+        <name>Protein alignment(Fastest speed)</name>\r
+        <description>\r
+            Fastest possible speed for protein sequences. Gives acceptable quality \r
+            alignments for closely related sequences\r
+        </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
+\r
+    <preset>\r
+        <name>Nucleotide alignment(Fastest speed)</name>\r
+        <description>\r
+        Fastest possible speed for nucleotide sequences. Gives acceptable quality \r
+        alignments for closely related sequences\r
+        </description>\r
+        <optlist>\r
+            <option>-maxiters 1</option>\r
+            <option>-diags</option>\r
+        </optlist>\r
+    </preset>\r
+\r
+    <preset>\r
+        <name>Large alignments (balanced)</name>\r
+        <description>\r
+        A large number of sequences (a few thousand), or very long sequences, then the default \r
+        settings of may be too slow for practical use. A good compromise between speed and \r
+        accuracy is to run just the first two iterations of the algorithm.\r
+        </description>\r
+        <optlist>\r
+            <option>-maxiters 2</option>\r
+        </optlist>\r
+    </preset>\r
 </presets>\r