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src/b/i/biopython-HEAD/Bio/Phylo/TreeConstruction.py   biopython(Download)
        dm = copy.deepcopy(distance_matrix)
        # init terminal clades
        clades = [BaseTree.Clade(None, name) for name in dm.names]
        # init minimum index
        min_i = 0
            clade2 = clades[min_j]
            inner_count += 1
            inner_clade = BaseTree.Clade(None, "Inner" + str(inner_count))
            inner_clade.clades.append(clade1)
            inner_clade.clades.append(clade2)
        dm = copy.deepcopy(distance_matrix)
        # init terminal clades
        clades = [BaseTree.Clade(None, name) for name in dm.names]
        # init node distance
        node_dist = [0] * len(dm)
            clade2 = clades[min_j]
            inner_count += 1
            inner_clade = BaseTree.Clade(None, "Inner" + str(inner_count))
            inner_clade.clades.append(clade1)
            inner_clade.clades.append(clade2)

src/b/i/biopython-HEAD/Bio/Phylo/Consensus.py   biopython(Download)
    strict_bitstrs.sort(key=lambda bitstr: bitstr.count('1'), reverse=True)
    # Create root
    root = BaseTree.Clade()
    if strict_bitstrs[0].count('1') == len(terms):
        root.clades.extend(terms)
    for bitstr in strict_bitstrs[1:]:
        clade_terms = [terms[i] for i in bitstr.index_one()]
        clade = BaseTree.Clade()
        clade.clades.extend(clade_terms)
        for bs, c in bitstr_clades.items():
                                         str(bitstr)),
                     reverse=True)
    root = BaseTree.Clade()
    if bitstrs[0].count('1') == len(terms):
        root.clades.extend(terms)
            break
        clade_terms = [terms[i] for i in bitstr.index_one()]
        clade = BaseTree.Clade()
        clade.clades.extend(clade_terms)
        clade.confidence = confidence
                        if independent:
                            bitstrs.add(ta)
        new_clade = BaseTree.Clade()
        for bitstr in sorted(bitstrs):
            indices = bitstr.index_one()

src/b/i/biopython-HEAD/Bio/Phylo/NeXML.py   biopython(Download)
class Clade(BaseTree.Clade):
    """NeXML Clade (sub-tree) object."""
 
    def __init__(self, branch_length=1.0, name=None, clades=None,
                 confidence=None, comment=None, **kwargs):

src/b/i/biopython-HEAD/Bio/Phylo/Newick.py   biopython(Download)
class Clade(BaseTree.Clade):
    """Newick Clade (sub-tree) object."""
 
    def __init__(self, branch_length=1.0, name=None, clades=None,
                 confidence=None, comment=None):

src/b/i/biopython-HEAD/Bio/Phylo/CDAO.py   biopython(Download)
class Clade(BaseTree.Clade):
    """CDAO Clade (sub-tree) object."""
 
    def __init__(self, branch_length=1.0, name=None, clades=None,
                 confidence=None, comment=None):

src/b/i/biopython-1.63/Bio/Phylo/NeXML.py   biopython(Download)
class Clade(BaseTree.Clade):
    """NeXML Clade (sub-tree) object."""
 
    def __init__(self, branch_length=1.0, name=None, clades=None,
                 confidence=None, comment=None, **kwargs):

src/b/i/biopython-1.63/Bio/Phylo/Newick.py   biopython(Download)
class Clade(BaseTree.Clade):
    """Newick Clade (sub-tree) object."""
 
    def __init__(self, branch_length=1.0, name=None, clades=None,
                 confidence=None, comment=None):

src/b/i/biopython-1.63/Bio/Phylo/CDAO.py   biopython(Download)
class Clade(BaseTree.Clade):
    """CDAO Clade (sub-tree) object."""
 
    def __init__(self, branch_length=1.0, name=None, clades=None,
                 confidence=None, comment=None):

src/b/i/biopython-HEAD/Bio/Phylo/PhyloXML.py   biopython(Download)
class Clade(PhyloElement, BaseTree.Clade):
    """Describes a branch of the current phylogenetic tree.
 
    Used recursively, describes the topology of a phylogenetic tree.
 

src/b/i/biopython-1.63/Bio/Phylo/PhyloXML.py   biopython(Download)
class Clade(PhyloElement, BaseTree.Clade):
    """Describes a branch of the current phylogenetic tree.
 
    Used recursively, describes the topology of a phylogenetic tree.