| Bio/Align/DNAStatistics.pm | |||
|---|---|---|---|
| Criterion | Covered | Total | % |
| subroutine | 39 | 45 | 86.6 |
| pod | 20 | 30 | 66.6 |
| line | count | pod | subroutine |
|---|---|---|---|
| 340 | 4 | n/a | BEGIN |
| 341 | 4 | n/a | BEGIN |
| 342 | 4 | n/a | BEGIN |
| 343 | 4 | n/a | BEGIN |
| 344 | 4 | n/a | BEGIN |
| 347 | 4 | n/a | BEGIN |
| 402 | 4 | n/a | BEGIN |
| 426 | 2 | Yes | new |
| 451 | 13 | Yes | distance |
| 480 | 0 | Yes | available_distance_methods |
| 504 | 2 | Yes | D_JukesCantor |
| 559 | 2 | Yes | D_F81 |
| 614 | 3 | Yes | D_Uncorrected |
| 678 | 2 | Yes | D_Kimura |
| 747 | 0 | Yes | D_Kimura_variance |
| 828 | 2 | Yes | D_Tamura |
| 910 | 0 | Yes | D_F84 |
| 962 | 2 | Yes | D_TajimaNei |
| 1069 | 0 | Yes | D_JinNei |
| 1087 | 6 | Yes | transversions |
| 1103 | 6 | Yes | transitions |
| 1109 | 12 | n/a | _trans_count_helper |
| 1136 | 19 | n/a | _build_nt_matrix |
| 1172 | 0 | n/a | _check_ambiguity_nucleotide |
| 1192 | 25 | n/a | _check_arg |
| 1219 | 18 | Yes | pairwise_stats |
| 1242 | 1 | Yes | calc_KaKs_pair |
| 1278 | 1 | Yes | calc_all_KaKs_pairs |
| 1305 | 1 | Yes | calc_average_KaKs |
| 1326 | 1 | n/a | _run_bootstrap |
| 1357 | 100 | n/a | _resample |
| 1377 | 103 | n/a | _get_av_ds_dn |
| 1456 | 614 | No | jk |
| 1466 | 8 | No | jk_var |
| 1475 | 307 | No | analyse_mutations |
| 1587 | 17499 | No | count_diffs |
| 1623 | 4 | Yes | get_syn_changes |
| 1667 | 0 | Yes | dnds_pattern_number |
| 1673 | 615 | No | count_syn_sites |
| 1689 | 4 | No | get_syn_sites |
| 1731 | 8 | n/a | _make_codons |
| 1745 | 4 | No | get_codons |
| 1756 | 204 | No | mean |
| 1764 | 2 | No | variance |
| 1772 | 2 | No | sampling_variance |