def get_dn_ds_matrix(self, method="NG86", codon_table=default_codon_table): """Available methods include NG86, LWL85, YN00 and ML. Argument: - method - Available methods include NG86, LWL85, YN00 and ML. - codon_table - Codon table to use for forward translation. """ from Bio.Phylo.TreeConstruction import _DistanceMatrix as DM names = [i.id for i in self._records] size = len(self._records) dn_matrix = [] ds_matrix = [] for i in range(size): dn_matrix.append([]) ds_matrix.append([]) for j in range(i + 1): if i != j: dn, ds = cal_dn_ds(self._records[i], self._records[j], method=method, codon_table=codon_table) dn_matrix[i].append(dn) ds_matrix[i].append(ds) else: dn_matrix[i].append(0.0) ds_matrix[i].append(0.0) dn_dm = DM(names, matrix=dn_matrix) ds_dm = DM(names, matrix=ds_matrix) return dn_dm, ds_dm
def get_dn_ds_matrix(self, method="NG86"): """Available methods include NG86, LWL85, YN00 and ML. """ from Bio.Phylo.TreeConstruction import _DistanceMatrix as DM names = [i.id for i in self._records] size = len(self._records) dn_matrix = [] ds_matrix = [] for i in range(size): dn_matrix.append([]) ds_matrix.append([]) for j in range(i + 1): if i != j: dn, ds = cal_dn_ds(self._records[i], self._records[j], method=method) dn_matrix[i].append(dn) ds_matrix[i].append(ds) else: dn_matrix[i].append(0.0) ds_matrix[i].append(0.0) dn_dm = DM(names, matrix=dn_matrix) ds_dm = DM(names, matrix=ds_matrix) return dn_dm, ds_dm