import org.forester.msa.ResampleableMsa;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.msa.ResampleableMsa;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
private final boolean DEBUG = true;
public final static String MSA_FILE_SUFFIX = ".aln";
public final static String PWD_FILE_SUFFIX = ".pwd";
private final boolean DEBUG = true;
public final static String MSA_FILE_SUFFIX = ".aln";
public final static String PWD_FILE_SUFFIX = ".pwd";
final PhylogeneticInferenceOptions options,
final MainFrameApplication mf ) {
_msa = null;
final PhylogeneticInferenceOptions options,
final MainFrameApplication mf ) {
_msa = null;
- private Msa runMAFFT( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
+ private Msa runMAFFT( final List<MolecularSequence> seqs, final List<String> opts ) throws IOException,
+ InterruptedException {