Table 4.
Results of a Code Duplication Analysis Using the Simian Tool.
| Code | Lines Checked | Files Checked | Duplicate Lines | Duplication % | Blocks | Files |
|---|---|---|---|---|---|---|
| PAML | 22,200 | 17 | 1,210 | 5.5% | 120 | 11 |
| PHYML | 42,786 | 73 | 5,878 | 13.7% | 549 | 32 |
| MrBayes | 70,680 | 19 | 21,862 | 30.9% | 1,680 | 10 |
| RAxML | 55,873 | 25 | 17,137 | 30.7% | 1,304 | 22 |
| SOAP | 27,514 | 116 | 10,107 | 36.7% | 527 | 72 |
| Abyss | 37,038 | 212 | 4,245 | 11.5% | 441 | 71 |
| MS | 1,718 | 24 | 186 | 10.8% | 21 | 9 |
| SweepFinder | 3,777 | 12 | 293 | 7.8% | 28 | 3 |
| MAFFT | 45,045 | 72 | 28,630 | 63.6% | 1,647 | 59 |
| T-Coffee | 82,758 | 196 | 19,345 | 23.4% | 1,325 | 58 |
| Prank | 16,124 | 67 | 5,318 | 33.0% | 462 | 43 |
| BEAST | 228,316 | 2,336 | 64,024 | 28.0% | 4,786 | 1,151 |
| BP&P | 14,332 | 5 | 502 | 3.5% | 56 | 3 |
| Seq-Gen | 3,244 | 44 | 206 | 6.4% | 25 | 6 |
| INDELible | 9,840 | 7 | 1,954 | 19.9% | 106 | 5 |
| Gadget-2 | 9,770 | 31 | 3,314 | 33.9% | 180 | 31 |
Note.—The column “Lines checked” refers to the total number of source lines and “Files checked” to the total number of source files analyzed with Simian. Note that, the “Lines checked” number is not identical to the LoC numbers reported in tables 2 and 3, since the Simian tool does not take header files into account. Column “Duplicate lines” provides the number of duplicate lines detected, “duplication %” the relative amount of code duplication, and “Blocks” provides the total number of contiguous duplicated blocks of code. Finally, column “Files” gives the number of files in which duplicated code was detected.