- a -

• a1 : bip_hashtable_struct , hashtable_struct
• a2 : hashtable_struct
• alloc : char_vector_struct

- b -

• b1 : hashtable_struct
• b2 : hashtable_struct
• bit32 : biomcmc_rng_struct
• blength : topology_struct
• branch_length : newick_node_struct
• bs : bipartition_struct

- c -

• character : alignment_struct
• charset_start : alignment_struct
• col_hash : binary_parsimony_datamatrix_struct
• col_mate : hungarian_struct
• count : bip_hashitem_struct , spdist_matrix_struct

- d -

• d : distance_matrix_struct
• d_done : topol_node_struct
• dcost : hungarian_struct
• dna : kmerhash_struct
• dup : reconciliation_struct

- e -

• estimate : hll_estimate_s

- f -

• filename : alignment_struct , topology_space_struct
• final_cost : hungarian_struct
• freq : distance_matrix_struct , topology_space_struct
• freq_sum : binary_parsimony_datamatrix_struct
• fromroot : distance_matrix_struct

- h -

• h : bip_hashtable_struct , hashtable_struct
• hashID1 : topology_struct
• have_bit32 : biomcmc_rng_struct
• have_rnorm32 : biomcmc_rng_struct
• hll_estimate : hll_estimate_s

- i -

• i : binary_parsimony_datamatrix_struct
• id : newick_node_struct , topol_node_struct , topology_struct
• idx : distance_matrix_struct
• index : topology_struct
• initial_cost : hungarian_struct
• internal : binary_parsimony_struct , topol_node_struct
• ints : bipsize_struct
• is_aligned : alignment_struct
• is_rooted : topology_space_struct

- k -

• key : hashtable_item_struct
• kmer_class_mode : kmer_params_struct

- l -

• large_range_estimate : hll_estimate_s
• leaflist : newick_tree_struct

- m -

• map_u : reconciliation_struct
• mask : bipsize_struct
• max : empfreq_double_struct , empfreq_struct
• maxfreq : bip_hashtable_struct
• mean_JC_dist : distance_matrix_struct
• mean_K2P_dist : distance_matrix_struct
• mean_R : distance_matrix_struct
• mid : topol_node_struct
• mt : biomcmc_rng_struct

- n -

• n : bipartition_struct
• n_buckets : hll_estimate_s
• n_charset : alignment_struct
• n_empty_buckets : hll_estimate_s
• n_g : splitset_struct
• n_hash : kmerhash_struct
• n_ones : bipartition_struct
• n_undone : topology_struct
• nchars : char_vector_struct
• ndcos : reconciliation_struct
• ndup_d : reconciliation_struct
• ndup_u : reconciliation_struct
• ndups : reconciliation_struct
• next_avail : char_vector_struct
• nleaves : topology_struct
• nlos_d : reconciliation_struct
• nlos_u : reconciliation_struct
• nloss : reconciliation_struct
• nnodes : newick_tree_struct , topology_struct
• nstrings : char_vector_struct

- o -

• occupancy : binary_parsimony_datamatrix_struct

- p -

• P : bip_hashtable_struct , hashtable_struct
• pattern_freq : alignment_struct
• postorder : topology_struct
• probelength : bip_hashtable_struct , hashtable_struct

- q -

• quasirandom : topology_struct

- r -

• ref_counter : alignment_struct , binary_parsimony_datamatrix_struct , binary_parsimony_struct , bip_hashtable_struct , bipartition_struct , bipsize_struct , char_vector_struct , distance_matrix_struct , empfreq_double_struct , empfreq_struct , hashtable_struct , newick_space_struct , spdist_matrix_struct , speciestree_struct , topology_struct
• rnorm32 : biomcmc_rng_struct
• root : newick_tree_struct , topology_struct
• row_dec_d : hungarian_struct

- s -

• s : binary_parsimony_datamatrix_struct
• score : binary_parsimony_struct
• site_pattern : alignment_struct
• size : hashtable_struct , hungarian_struct
• size_diff : reconciliation_struct
• small_range_estimate : hll_estimate_s
• sp_count : reconciliation_struct
• sp_id : reconciliation_struct
• sp_size : reconciliation_struct
• species_present : spdist_matrix_struct
• split : topol_node_struct
• spnames_order : speciestree_struct

- t -

• t : newick_space_struct
• table : hashtable_struct
• taxlabel : alignment_struct , newick_node_struct , topology_space_struct , topology_struct
• taxlabel_hash : alignment_struct , topology_space_struct
• taxshort : alignment_struct
• traversal_updated : topology_struct
• tree : topology_space_struct

- u -

• u_done : topol_node_struct
• undo_lca : topology_struct
• undo_prune : topology_struct
• undo_regraft : topology_struct
• undone : topology_struct

- v -

• value : hashtable_item_struct
• var_K2P_dist : distance_matrix_struct
• var_R : distance_matrix_struct