import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
outfile = new File( args[ 1 ] );
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
outfile = new File( args[ 1 ] );
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
tree = factory.create( infile, pp )[ 0 ];
}
catch ( final Exception e ) {
tree = factory.create( infile, pp )[ 0 ];
}
catch ( final Exception e ) {