import javax.swing.JOptionPane;
import org.forester.archaeopteryx.MainFrameApplication;
-import org.forester.evoinference.distance.NeighborJoining;
+import org.forester.evoinference.distance.NeighborJoiningF;
import org.forester.evoinference.distance.PairwiseDistanceCalculator;
import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
import org.forester.evoinference.tools.BootstrapResampler;
e.printStackTrace();
}
}
- final NeighborJoining nj = NeighborJoining.createInstance();
+ final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 );
final Phylogeny phy = nj.execute( m );
PhylogenyMethods.extractFastaInformation( phy );
return phy;
import org.forester.evoinference.distance.NeighborJoining;
import org.forester.evoinference.distance.NeighborJoiningF;
-import org.forester.evoinference.distance.NeighborJoiningX;
import org.forester.evoinference.distance.PairwiseDistanceCalculator;
import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
return true;
}
- private static boolean testDistanceCalculationMethods( final File test_dir ) {
- try {
- final Msa msa0 = GeneralMsaParser.parse( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR
- + "bcl.aln" ) );
- final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 );
- if ( pwd0.getSize() != 120 ) {
- return false;
- }
- for( int i = 0; i < pwd0.getSize(); ++i ) {
- if ( !isEqual( pwd0.getValue( i, i ), 0.0 ) ) {
- return false;
- }
- }
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
private static boolean testBasicCharacterStateMatrix() {
try {
final CharacterStateMatrix<String> matrix_0 = new BasicCharacterStateMatrix<String>( 4, 8 );
return true;
}
+ private static boolean testDistanceCalculationMethods( final File test_dir ) {
+ try {
+ final Msa msa0 = GeneralMsaParser.parse( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR
+ + "bcl.aln" ) );
+ final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 );
+ if ( pwd0.getSize() != 120 ) {
+ return false;
+ }
+ for( int i = 0; i < pwd0.getSize(); ++i ) {
+ if ( !isEqual( pwd0.getValue( i, i ), 0.0 ) ) {
+ return false;
+ }
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testDolloParsimony() {
try {
final BinaryStates PRESENT = BinaryStates.PRESENT;
private static boolean testNeighborJoining() {
try {
- final NeighborJoiningF njf = NeighborJoiningF.createInstance();
- final BasicSymmetricalDistanceMatrix m0f = new BasicSymmetricalDistanceMatrix( 4 );
- m0f.setIdentifier( 0, "A" );
- m0f.setIdentifier( 1, "B" );
- m0f.setIdentifier( 2, "C" );
- m0f.setIdentifier( 3, "D" );
- m0f.setRow( "5 ", 1 );
- m0f.setRow( "3 6 ", 2 );
- m0f.setRow( "7.5 10.5 5.5", 3 );
- final Phylogeny p0f = njf.execute( m0f );
- p0f.reRoot( p0f.getNode( "D" ) );
- if ( isUnequal( p0f.getNode( "A" ).getDistanceToParent(), 1 ) ) {
- return false;
- }
- if ( isUnequal( p0f.getNode( "B" ).getDistanceToParent(), 4 ) ) {
- return false;
- }
- if ( isUnequal( p0f.getNode( "C" ).getDistanceToParent(), 0.5 ) ) {
- return false;
- }
- if ( isUnequal( p0f.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
- return false;
- }
- if ( isUnequal( p0f.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) {
- return false;
- }
- if ( isUnequal( p0f.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) {
- return false;
- }
- //
NeighborJoining nj = NeighborJoining.createInstance();
final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 );
m0.setIdentifier( 0, "A" );
if ( isUnequal( p3.getNode( "A" ).getParent().getParent().getDistanceToParent(), 0.05 ) ) {
return false;
}
- //if ( TIME ) {
- // timeNeighborJoining();
- //}
+ //
+ NeighborJoiningF njf = NeighborJoiningF.createInstance();
+ final BasicSymmetricalDistanceMatrix m0f = new BasicSymmetricalDistanceMatrix( 4 );
+ m0f.setIdentifier( 0, "A" );
+ m0f.setIdentifier( 1, "B" );
+ m0f.setIdentifier( 2, "C" );
+ m0f.setIdentifier( 3, "D" );
+ m0f.setRow( "5 ", 1 );
+ m0f.setRow( "3 6 ", 2 );
+ m0f.setRow( "7.5 10.5 5.5", 3 );
+ final Phylogeny p0f = njf.execute( m0f );
+ p0f.reRoot( p0f.getNode( "D" ) );
+ if ( isUnequal( p0f.getNode( "A" ).getDistanceToParent(), 1 ) ) {
+ return false;
+ }
+ if ( isUnequal( p0f.getNode( "B" ).getDistanceToParent(), 4 ) ) {
+ return false;
+ }
+ if ( isUnequal( p0f.getNode( "C" ).getDistanceToParent(), 0.5 ) ) {
+ return false;
+ }
+ if ( isUnequal( p0f.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
+ return false;
+ }
+ if ( isUnequal( p0f.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) {
+ return false;
+ }
+ if ( isUnequal( p0f.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) {
+ return false;
+ }
+ //
+ m = new BasicSymmetricalDistanceMatrix( 7 );
+ m.setIdentifier( 0, "Bovine" );
+ m.setIdentifier( 1, "Mouse" );
+ m.setIdentifier( 2, "Gibbon" );
+ m.setIdentifier( 3, "Orang" );
+ m.setIdentifier( 4, "Gorilla" );
+ m.setIdentifier( 5, "Chimp" );
+ m.setIdentifier( 6, "Human" );
+ m.setRow( "0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050", 0 );
+ m.setRow( "1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290", 1 );
+ m.setRow( "1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830", 2 );
+ m.setRow( "1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100", 3 );
+ m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 );
+ m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 );
+ m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 );
+ njf = NeighborJoiningF.createInstance( false, 5 );
+ final Phylogeny p2f = njf.execute( m );
+ p2f.reRoot( p2f.getNode( "Bovine" ) );
+ if ( isUnequal( p2f.getNode( "Chimp" ).getDistanceToParent(), 0.15168 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2f.getNode( "Human" ).getDistanceToParent(), 0.11752 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2f.getNode( "Gorilla" ).getDistanceToParent(), 0.15393 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2f.getNode( "Orang" ).getDistanceToParent(), 0.28469 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2f.getNode( "Gibbon" ).getDistanceToParent(), 0.35793 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2f.getNode( "Mouse" ).getDistanceToParent(), 0.76891 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2f.getNode( "Bovine" ).getDistanceToParent(), 0.458845 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getDistanceToParent(), 0.03982 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2f.getNode( "Human" ).getParent().getDistanceToParent(), 0.03982 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getDistanceToParent(), 0.02696 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getDistanceToParent(), 0.04648 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent()
+ .getDistanceToParent(), 0.42027 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent()
+ .getDistanceToParent(), 0.458845 ) ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
private static void timeNeighborJoining() {
final NeighborJoiningF njf = NeighborJoiningF.createInstance();
- for( int n = 3; n <= 10; ++n ) {
+ for( int n = 3; n <= 8; ++n ) {
final int x = ( int ) Math.pow( 2, n );
final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x );
mt.randomize( new Date().getTime() );
- // for( int i = 0; i < mt.getSize(); i++ ) {
- // mt.setIdentifier( i, i + "i" );
- // }
- // System.out.println( mt.toStringBuffer( Format.PHYLIP ) );
final long start_time = new Date().getTime();
njf.execute( mt );
System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" );
}
final NeighborJoining nj = NeighborJoining.createInstance();
- for( int n = 3; n <= 10; ++n ) {
+ for( int n = 3; n <= 8; ++n ) {
final int x = ( int ) Math.pow( 2, n );
final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x );
mt.randomize( new Date().getTime() );
- // for( int i = 0; i < mt.getSize(); i++ ) {
- // mt.setIdentifier( i, i + "i" );
- // }
- // System.out.println( mt.toStringBuffer( Format.PHYLIP ) );
final long start_time = new Date().getTime();
nj.execute( mt );
System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" );
}
- final NeighborJoiningX njx = NeighborJoiningX.createInstance();
- for( int n = 3; n <= 10; ++n ) {
- final int x = ( int ) Math.pow( 2, n );
- final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x );
- mt.randomize( new Date().getTime() );
- // for( int i = 0; i < mt.getSize(); i++ ) {
- // mt.setIdentifier( i, i + "i" );
- // }
- // System.out.println( mt.toStringBuffer( Format.PHYLIP ) );
- final long start_time = new Date().getTime();
- njx.execute( mt );
- System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" );
- }
}
}
}
}
- private final void printD() {
- System.out.println( "D:" );
- for( final double[] _d_value : _d_values ) {
- for( int j = 0; j < _d_values.length; j++ ) {
- System.out.print( _d_value[ j ] );
- System.out.print( " " );
- }
- System.out.println();
- }
- System.out.println();
- }
-
- private final void printM() {
- System.out.println( "M:" );
- for( final double[] _m_value : _m_values ) {
- for( int j = 0; j < _m_values.length; j++ ) {
- System.out.print( _m_value[ j ] );
- System.out.print( " " );
- }
- System.out.println();
- }
- System.out.println();
- }
-
private final void printProgress( final int otu1, final int otu2 ) {
final PhylogenyNode n1 = getExternalPhylogenyNode( otu1 );
final PhylogenyNode n2 = getExternalPhylogenyNode( otu2 );
}
// only the values in the lower triangle are used.
- // !matrix values will be changed!
private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
_n = distances.getSize();
_d = distances;
+++ /dev/null
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
-
-package org.forester.evoinference.distance;
-
-import java.math.RoundingMode;
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.util.ForesterUtil;
-
-public final class NeighborJoiningX {
-
- private BasicSymmetricalDistanceMatrix _d;
- private double[][] _d_values;
- private final DecimalFormat _df;
- private PhylogenyNode[] _external_nodes;
- private double[][] _m_values;
- private int[] _mappings;
- private int _n;
- private double[] _r;
- private final boolean _verbose;
-
- private NeighborJoiningX() {
- _verbose = false;
- _df = null;
- }
-
- private NeighborJoiningX( final boolean verbose, final int maximum_fraction_digits_for_distances ) {
- if ( ( maximum_fraction_digits_for_distances < 1 ) || ( maximum_fraction_digits_for_distances > 9 ) ) {
- throw new IllegalArgumentException( "maximum fraction digits for distances is out of range: "
- + maximum_fraction_digits_for_distances );
- }
- _verbose = verbose;
- _df = new DecimalFormat();
- _df.setMaximumFractionDigits( maximum_fraction_digits_for_distances );
- _df.setRoundingMode( RoundingMode.HALF_UP );
- }
-
- public final Phylogeny execute( final BasicSymmetricalDistanceMatrix distance ) {
- reset( distance );
- final Phylogeny phylogeny = new Phylogeny();
- while ( _n > 2 ) {
- updateM();
- // Calculates the minimal distance.
- // If more than one minimal distances, always the first found is used
- // could randomize this, so that any would be returned in a randomized fashion...
- double minimum = _m_values[ 0 ][ 1 ];
- int otu1 = 0;
- int otu2 = 1;
- for( int j = 1; j < _n; ++j ) {
- for( int i = 0; i < j; ++i ) {
- if ( _m_values[ i ][ j ] < minimum ) {
- minimum = _m_values[ i ][ j ];
- otu1 = i;
- otu2 = j;
- }
- }
- }
- // It is a condition that otu1 < otu2.
- final PhylogenyNode node = new PhylogenyNode();
- final double d = getValueFromD( otu1, otu2 );
- final double d1 = ( d / 2 ) + ( ( _r[ otu1 ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) );
- final double d2 = d - d1;
- if ( _df == null ) {
- getExternalPhylogenyNode( otu1 ).setDistanceToParent( d1 );
- getExternalPhylogenyNode( otu2 ).setDistanceToParent( d2 );
- }
- else {
- // yes, yes, slow but only grows with n (and not n^2 or worse)...
- getExternalPhylogenyNode( otu1 ).setDistanceToParent( Double.parseDouble( _df.format( d1 ) ) );
- getExternalPhylogenyNode( otu2 ).setDistanceToParent( Double.parseDouble( _df.format( d2 ) ) );
- }
- node.addAsChild( getExternalPhylogenyNode( otu1 ) );
- node.addAsChild( getExternalPhylogenyNode( otu2 ) );
- if ( _verbose ) {
- printProgress( otu1, otu2 );
- }
- calculateDistancesFromNewNode( otu1, otu2, d );
- _external_nodes[ _mappings[ otu1 ] ] = node;
- updateMappings( otu2 );
- --_n;
- }
- final double d = getValueFromD( 0, 1 ) / 2;
- if ( _df == null ) {
- getExternalPhylogenyNode( 0 ).setDistanceToParent( d );
- getExternalPhylogenyNode( 1 ).setDistanceToParent( d );
- }
- else {
- final double dd = Double.parseDouble( _df.format( d ) );
- getExternalPhylogenyNode( 0 ).setDistanceToParent( dd );
- getExternalPhylogenyNode( 1 ).setDistanceToParent( dd );
- }
- final PhylogenyNode root = new PhylogenyNode();
- root.addAsChild( getExternalPhylogenyNode( 0 ) );
- root.addAsChild( getExternalPhylogenyNode( 1 ) );
- if ( _verbose ) {
- printProgress( 0, 1 );
- }
- phylogeny.setRoot( root );
- phylogeny.setRooted( false );
- return phylogeny;
- }
-
- public final List<Phylogeny> execute( final List<BasicSymmetricalDistanceMatrix> distances_list ) {
- final List<Phylogeny> pl = new ArrayList<Phylogeny>();
- for( final BasicSymmetricalDistanceMatrix distances : distances_list ) {
- pl.add( execute( distances ) );
- }
- return pl;
- }
-
- private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) {
- for( int i = 0; i < _n; ++i ) {
- if ( ( i == otu1 ) || ( i == otu2 ) ) {
- continue;
- }
- if ( otu1 < i ) {
- _d_values[ _mappings[ otu1 ] ][ _mappings[ i ] ] = ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2;
- }
- else {
- _d_values[ _mappings[ i ] ][ _mappings[ otu1 ] ] = ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2;
- }
- }
- }
-
- private final void calculateNetDivergences() {
- double d;
- for( int i = 0; i < _n; ++i ) {
- d = 0;
- for( int n = 0; n < _n; ++n ) {
- if ( i != n ) {
- d += getValueFromD( i, n );
- }
- }
- _r[ i ] = d;
- }
- }
-
- private final PhylogenyNode getExternalPhylogenyNode( final int i ) {
- return _external_nodes[ _mappings[ i ] ];
- }
-
- private final double getValueFromD( final int otu1, final int otu2 ) {
- if ( otu1 > otu2 ) {
- return _d_values[ _mappings[ otu2 ] ][ _mappings[ otu1 ] ];
- }
- return _d_values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ];
- }
-
- private final void initExternalNodes() {
- _external_nodes = new PhylogenyNode[ _n ];
- String id;
- for( int i = 0; i < _n; ++i ) {
- _external_nodes[ i ] = new PhylogenyNode();
- id = _d.getIdentifier( i );
- if ( id != null ) {
- _external_nodes[ i ].setName( id );
- }
- else {
- _external_nodes[ i ].setName( "" + i );
- }
- _mappings[ i ] = i;
- }
- }
-
- private final void printProgress( final int otu1, final int otu2 ) {
- final PhylogenyNode n1 = getExternalPhylogenyNode( otu1 );
- final PhylogenyNode n2 = getExternalPhylogenyNode( otu2 );
- System.out.println( "Node " + ( ForesterUtil.isEmpty( n1.getName() ) ? n1.getId() : n1.getName() ) + " joins "
- + ( ForesterUtil.isEmpty( n2.getName() ) ? n2.getId() : n2.getName() ) );
- }
-
- // only the values in the lower triangle are used.
- // !matrix values will be changed!
- private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
- _n = distances.getSize();
- _d = distances;
- _r = new double[ _n ];
- _mappings = new int[ _n ];
- _d_values = _d.getValues();
- _m_values = new double[ _n ][ _n ];
- initExternalNodes();
- }
-
- private final void updateM() {
- calculateNetDivergences();
- for( int j = 1; j < _n; ++j ) {
- for( int i = 0; i < j; ++i ) {
- _m_values[ i ][ j ] = getValueFromD( i, j ) - ( ( _r[ i ] + _r[ j ] ) / ( _n - 2 ) );
- }
- }
- }
-
- // otu2 will, in effect, be "deleted" from the matrix.
- private final void updateMappings( final int otu2 ) {
- for( int i = otu2; i < ( _mappings.length - 1 ); ++i ) {
- _mappings[ i ] = _mappings[ i + 1 ];
- }
- }
-
- public final static NeighborJoiningX createInstance() {
- return new NeighborJoiningX();
- }
-
- public final static NeighborJoiningX createInstance( final boolean verbose,
- final int maximum_fraction_digits_for_distances ) {
- return new NeighborJoiningX( verbose, maximum_fraction_digits_for_distances );
- }
-}
// NumberFormat nf1 = NumberFormat.getInstance();
private final static NumberFormat PHYLIP_FORMATTER = new DecimalFormat( "0.000000" );
- final double[][] _values;
final String[] _identifiers;
+ final double[][] _values;
public BasicSymmetricalDistanceMatrix( final int size ) {
_values = new double[ size ][ size ];
_identifiers = new String[ size ];
}
- public final double[][] getValues() {
- return _values;
- }
-
@Override
public final String getIdentifier( final int i ) {
return _identifiers[ i ];
return _values[ col ][ row ];
}
+ public final double[][] getValues() {
+ return _values;
+ }
+
public final void randomize( final long seed ) {
final java.util.Random r = new java.util.Random( seed );
for( int j = 0; j < getSize(); ++j ) {
_values[ col ][ row ] = d;
}
+ @Override
+ public final String toString() {
+ return toPhylip().toString();
+ }
+
+ @Override
+ public final StringBuffer toStringBuffer( final Format format ) {
+ switch ( format ) {
+ case PHYLIP:
+ return toPhylip();
+ default:
+ throw new IllegalArgumentException( "Unknown format:" + format );
+ }
+ }
+
public final void write( final Writer w ) throws IOException {
w.write( " " );
w.write( getSize() + "" );
}
return sb;
}
-
- @Override
- public final String toString() {
- return toPhylip().toString();
- }
-
- @Override
- public final StringBuffer toStringBuffer( final Format format ) {
- switch ( format ) {
- case PHYLIP:
- return toPhylip();
- default:
- throw new IllegalArgumentException( "Unknown format:" + format );
- }
- }
}
import java.util.TreeSet;
import org.forester.archaeopteryx.Archaeopteryx;
-import org.forester.evoinference.distance.NeighborJoining;
+import org.forester.evoinference.distance.NeighborJoiningF;
import org.forester.evoinference.distance.PairwiseDistanceCalculator;
import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
e.printStackTrace();
}
}
- final NeighborJoining nj = NeighborJoining.createInstance();
+ final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 );
final Phylogeny phy = nj.execute( m );
return phy;
}
git://source.jalview.org / jalview.git / commitdiff