X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FMsaCompactor.java;h=a66c09b2dc6068e5c16b8e5639c40ca4ef47ea2d;hb=ea402c168ecf73c1824d023a91331494939f2641;hp=9529b824ce71e0e0e8f24a1b7ddc306cd0823c26;hpb=e69287d798dd6fc6a0c3c257b5f4fc6507be9382;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/MsaCompactor.java b/forester/java/src/org/forester/msa/MsaCompactor.java
index 9529b82..a66c09b 100644
--- a/forester/java/src/org/forester/msa/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa/MsaCompactor.java
@@ -82,9 +82,9 @@ public class MsaCompactor {
     final private void mafft() throws IOException, InterruptedException {
         final MsaInferrer mafft = Mafft.createInstance( "/home/czmasek/bin/mafft" );
         final List<String> opts = new ArrayList<String>();
-        opts.add( "--maxiterate" );
-        opts.add( "1000" );
-        opts.add( "--localpair" );
+        // opts.add( "--maxiterate" );
+        // opts.add( "1000" );
+        // opts.add( "--localpair" );
         opts.add( "--quiet" );
         _msa = mafft.infer( _msa.asSequenceList(), opts );
     }