int choose_SPR_target(SequenceTree& T1, int b1_)
{
const_branchview b1 = T1.directed_branch(b1_);
//----- Select the branch to move to ------//
dynamic_bitset<> subtree_nodes = T1.partition(b1.reverse());
subtree_nodes[b1.target()] = true;
vector<int> branches;
vector<double> lengths;
for(int i=0; i<T1.n_branches(); i++)
{
const_branchview bi = T1.branch(i);
// skip branch if its contained in the subtree
if (subtree_nodes[bi.target()] and
subtree_nodes[bi.source()])
continue;
double L = 1.0;
// down-weight branch if it is one of the subtree's 2 neighbors
if (subtree_nodes[bi.target()] or
subtree_nodes[bi.source()])
L = 0.5;
branches.push_back(i);
lengths.push_back(L);
}
int b2 = branches[ choose(lengths) ];
return b2;
}
Partition partition_from_branch(const SequenceTree& T,int b)
{
dynamic_bitset<> group(T.n_leaves());
const dynamic_bitset<>& with_internal = T.partition(b);
for(int i=0;i<group.size();i++)
group[i] = with_internal[i];
return Partition(T.get_leaf_labels(), group);
}