dnaml-erate.c:  tree->likelihood = sum;
dnaml-erate.c:  tree->likelihood = oldlike;
dnaml-erate.c:    tree->likelihood = bestyet;
dnaml-erate.c:    if (q == tree->start)
dnaml-erate.c:  double oldbestyet = tree->likelihood;
dnaml-erate.c:  bestyet = tree->likelihood;
dnaml-erate.c:    num_sibs = count_sibs_erate(tree->nodep[i]);
dnaml-erate.c:    sib_ptr  = tree->nodep[i];
dnaml-erate.c:    tree->likelihood = bestyet;
dnaml-erate.c:        tree->likelihood = bestyet;
dnaml-erate.c:    if (p == tree->start)
dnaml-erate.c:  } while ((p == tree->start || p != q) &&
dnaml-erate.c:           (p != tree->start || p->next != q));
dnaml-erate.c:  if (p == tree->start)
dnaml-erate.c:  dnaml_coordinates_erate(tree, tree->start, 0.0, &tipy, &tipmax, ratfracchange);
dnaml-erate.c:  fprintf(outfile, "Ln Likelihood = %11.5f\n", tree->likelihood);
dnaml-erate.c:    if (tree->nodep[i]) {
dnaml-erate.c:      num_sibs = count_sibs_erate (tree->nodep[i]);
dnaml-erate.c:      sib_ptr  = tree->nodep[i];
dnaml-erate.c:  describe_erate(tree, table_erate, tree->start->back, tol);
dnaml-erate.c:  num_sibs = count_sibs_erate (tree->start);
dnaml-erate.c:  sib_ptr  = tree->start;
dnaml-erate.c:  dummy = evaluate_erate(tree, tree->start, table_erate, false, &root_data, tol);
dnaml-erate.c:      rectrav_erate(tree->start, i, k);
dnaml-erate.c:      rectrav_erate(tree->start->back, i, k);
dnaml-erate.c:    } while ((p == tree->start || p != q) &&
dnaml-erate.c:             (p != tree->start || p->next != q));
dnaml-erate.c:  if (p == tree->start)
dnaml-erate.c:  inittravtree_erate(tree->start);
dnaml-erate.c:    smooth_erate (tree, tree->start, table_erate, tol);
dnaml-erate.c:  dummy = evaluate_erate(tree, tree->start, table_erate, true, root_data, tol);
dnaml-erate.c:    tree->nodep[spp] = q;
dnaml-erate.c:		     tree->nodep, &nextnode, &haslengths, &grbg_erate, 
dnaml-erate.c:      dnaml_unroot_erate(endsite_erate, tree, root, tree->nodep, nonodes2);
dnaml-erate.c:      tree->start = tree->nodep[0]->back;
dnaml-erate.c:        tree->start = tree->nodep[outgrno - 1]->back;
dnaml-erate.c:        dnaml_treeout_erate(tree, tree->start, table_erate);
dnaml-erate.c:        freexe_notip(nextnode, tree->nodep);
dnaml-erate.c:        gdispose_erate(tree->start, &grbg_erate, tree->nodep);
dnaml-erate.c:    tree->start = tree->nodep[enterorder[0] - 1]->back;
dnaml-erate.c:        if (besttree2->likelihood < besttree->likelihood)
dnaml-erate.c:      tree->start = tree->nodep[outgrno - 1]->back;
dnaml-erate.c:          tree->nodep[i]->initialized = false;
dnaml-erate.c:          tree->nodep[i]->initialized = false;
dnaml-erate.c:          tree->nodep[i]->next->initialized = false;
dnaml-erate.c:          tree->nodep[i]->next->next->initialized = false;
dnaml-erate.c:        dnaml_treeout_erate(tree, tree->start, table_erate);
dnaml-erate.c:  freexe(nonodes2, tree->nodep);
dnaml-erate.c:    freexe(nonodes2, besttree->nodep);
dnaml-erate.c:    freexe(nonodes2, priortree->nodep);
dnaml-erate.c:  addtraverse_erate(tree, besttree, priortree, table_erate, tree->nodep[enterorder[nextsp - 1] - 1]->back,
dnaml-erate.c:		    tree->start, true, tol);
dnaml-erate.c:    insert_erate_(tree, table_erate, tree->nodep[enterorder[nextsp - 1] - 1]->back, qwhere_erate, true, tol);
dnaml-erate.c:      smooth_erate (tree, tree->start, table_erate, tol);
dnaml-erate.c:      smooth_erate (tree, tree->start->back, table_erate, tol);
dnaml-erate.c:    bestyet = tree->likelihood;
dnaml-erate.c:      rearrange_erate(tree, besttree, priortree, table_erate, tree->start, tree->start->back, tol);
dnaml-erate.c:  likelihood = evaluate_erate(data->tree, data->tree->start, data->table_erate, true, data->root_data, data->tol);
dnaml-erate.c:  tree->likelihood = -fx;
dnaml-erate.c:    printf("At maximum: lnlikelihood = %f\n", tree->likelihood);
dnaml-erate.c:  inittravtree_erate(data->tree->start);
dnaml-erate.c:    smooth_erate(data->tree, data->tree->start, data->table_erate, data->tol);
dnaml-erate.c:  likelihood = evaluate_erate(data->tree, data->tree->start, data->table_erate, true, data->root_data, data->tol);
dnaml-erate.c:  tree->likelihood = -fx;
dnaml-erate.c:    printf("At maximum: lnlikelihood = %f\n", tree->likelihood);
phylip-erate.c:     This is the main (new) tree-reading procedure */
phylip-erate.c:     This is the main (new) tree-reading procedure */
seq-erate.c:  if (!subtree->tip) {
seq-erate.c:    p = subtree->next;
seq-erate.c:         !((p->back->collapse == nocollap) && (subtree->collapse == nocollap))
seq-erate.c:           && (subtree->numdesc != 1)) {
seq-erate.c:        if ((p->back->collapse == tocollap) && (subtree->collapse == tocollap)
seq-erate.c:    p = subtree->next;
seq-erate.c:      if(i % (((oldnextree-1) / 72) + 1) == 0)
seq-erate.c:    findtree(&found, &pos, nextree-1, place, bestrees);    
seq-erate.c:    nextree--;
