log_double_t correction(const data_partition& P,const vector<int>& nodes)
{
if (P.variable_alignment())
{
// get the lengths of then internal node
int length = P.seqlength(nodes[0]);
return pow(P.sequence_length_pr(length), 2);
}
else
return 1;
}
efloat_t prior_HMM_rootless_scale(const data_partition& P)
{
const Tree& T = *P.T;
#ifndef NDEBUG
assert(P.has_IModel());
check_internal_nodes_connected(*P.A,T);
#endif
efloat_t Pr = 1;
for(int i=T.n_leaves();i<T.n_nodes();i++) {
int l = P.seqlength(i);
efloat_t temp = P.IModel().lengthp(l);
Pr /= (temp*temp);
}
return Pr;
}