|
Functions |
| Boolean | transition (sint base1, sint base2) |
| void | tree_gap_delete (void) |
| void | distance_matrix_output (FILE *ofile) |
| void | nj_tree (char **tree_description, FILE *tree) |
| void | compare_tree (char **tree1, char **tree2, sint *hits, sint n) |
| void | print_phylip_tree (char **tree_description, FILE *tree, sint bootstrap) |
| void | print_nexus_tree (char **tree_description, FILE *tree, sint bootstrap) |
| sint | two_way_split (char **tree_description, FILE *tree, sint start_row, sint flag, sint bootstrap) |
| sint | two_way_split_nexus (char **tree_description, FILE *tree, sint start_row, sint flag, sint bootstrap) |
| void | print_tree (char **tree_description, FILE *tree, sint *totals) |
| static Boolean | is_ambiguity (char c) |
| static void | overspill_message (sint overspill, sint total_dists) |
| void | phylogenetic_tree (char *phylip_name, char *clustal_name, char *dist_name, char *nexus_name, char *pim_name) |
| void | fast_nj_tree (char **tree_description, FILE *tree) |
| void | bootstrap_tree (char *phylip_name, char *clustal_name, char *nexus_name) |
| sint | dna_distance_matrix (FILE *tree) |
| sint | prot_distance_matrix (FILE *tree) |
| void | guide_tree (FILE *tree, sint firstseq, sint numseqs) |
Variables |
| sint | max_names |
| double ** | tmat |
| Boolean | dnaflag |
| Boolean | tossgaps |
| Boolean | kimura |
| Boolean | output_tree_clustal |
| Boolean | output_tree_phylip |
| Boolean | output_tree_distances |
| Boolean | output_tree_nexus |
| Boolean | output_pim |
| sint | bootstrap_format |
| Boolean | empty |
| Boolean | usemenu |
| sint | nseqs |
| sint | max_aln_length |
| sint * | seqlen_array |
| char ** | seq_array |
| char ** | names |
| char | seqname [] |
| sint | gap_pos1 |
| sint | gap_pos2 |
| Boolean | use_ambiguities |
| char * | amino_acid_codes |
| static double * | av |
| static double * | left_branch |
| static double * | right_branch |
| static double * | save_left_branch |
| static double * | save_right_branch |
| static sint * | boot_totals |
| static sint * | tkill |
| static sint * | boot_positions |
| static FILE * | phylip_phy_tree_file |
| static FILE * | clustal_phy_tree_file |
| static FILE * | distances_phy_tree_file |
| static FILE * | nexus_phy_tree_file |
| static FILE * | pim_file |
| static Boolean | verbose |
| static char * | tree_gaps |
| static sint | first_seq |
| static sint | last_seq |
| sint | boot_ntrials |
| unsigned sint | boot_ran_seed |
