final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( gene_trees_file, true );
if ( p instanceof NHXParser ) {
final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( false );
nhx.setIgnoreQuotes( true );
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( gene_trees_file, true );
if ( p instanceof NHXParser ) {
final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( false );
nhx.setIgnoreQuotes( true );