added -rs option

[jalview.git] / forester / java / src / org / forester / application / nj.java

diff --git a/forester/java/src/org/forester/application/nj.java b/forester/java/src/org/forester/application/nj.java
index 6bce553..dca5d08 100644 (file)
--- a/forester/java/src/org/forester/application/nj.java
+++ b/forester/java/src/org/forester/application/nj.java
@@ -22,7 +22,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.application;
 
@@ -119,7 +119,7 @@ public class nj {
                     + matrices[ 0 ].getSize() );
         }
         final List<Phylogeny> ps = new ArrayList<Phylogeny>();
-        final NeighborJoining nj = NeighborJoining.createInstance( verbose );
+        final NeighborJoining nj = NeighborJoining.createInstance( verbose, 6 );
         final long start_time = new Date().getTime();
         for( final DistanceMatrix matrix : matrices ) {
             ps.add( nj.execute( ( BasicSymmetricalDistanceMatrix ) matrix ) );
@@ -142,7 +142,7 @@ public class nj {
         System.out.println( "Usage:" );
         System.out.println();
         System.out.println( "% java -cp forester.jar org.forester.applications." + PRG_NAME
-                + " [options] <pairwise distances infile> <out file>" );
+                            + " [options] <pairwise distances infile> <out file>" );
         System.out.println();
         System.out.println( " Options: " );
         System.out.println( VERBOSE_OPTION + ": verbose on" );