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Table 5 Values of the six criteria for the FS dataset

From: Aligning coding sequences with frameshift extension penalties

fs_open_ cost fs_extend_cost (# CDS pairs) Method Identity_ NT Identity_ AA Gap_ init Gap_ length FS_init (avg) FS_ length
−10 −1 (212) fse0 166002 325212 895 60662 226 (1.06 ± 0.25) 20219
fse 165720 325026 901 60624 216 (1.01 ± 0.14) 18705
macse_p 166167 324999 1445 61562 432 (2.03 ± 3.06) 22742
needlenuc 172959 321348 5053 60038 2103 (9.91 ± 26.73) 29616
−0.5 (386) fse0 252590 464712 2400 114859 482 (1.24 ± 0.47) 31777
fse 251647 463407 2387 115269 401 (1.03 ± 0.19) 26982
macse_p 253715 465594 4161 117165 1306 (3.38 ± 4.53) 41742
needlenuc 279682 452673 19408 113195 8032 (20.80 ± 31.02) 68226
−0.2 (619) fse0 371062 641748 5334 204370 805 (1.30 ± 0.52) 43381
fse 370260 640377 5270 204806 688 (1.11 ± 0.33) 37376
macse_p 374729 646893 9308 208344 2893 (4.67 ± 5.34) 72030
needlenuc 442564 618270 48799 209420 19751 (31.90 ± 34.48) 141217
−20 −1 (161) fse0 123814 244350 461 40315 168 (1.04 ± 0.20) 17770
fse 123610 244149 468 40195 164 (1.01 ± 0.14) 16924
macse_p 123541 243591 709 40585 223 (1.38 ± 1.03) 18119
needlenuc 125452 242742 1493 39031 650 (4.03 ± 5.85) 19405
−0.5 (189) fse0 147476 291147 549 49485 197 (1.04 ± 0.20) 19599
fse 147401 291048 557 49363 194 (1.02  ± 0.16 ) 19279
macse_p 147143 290271 838 49841 260 (1.37 ± 0.98) 19976
needlenuc 149551 289086 1872 47515 808 (4.27 ± 6.17) 21440
−0.2 (216) fse0 161906 318117 723 55383 225 (1.04 ± 0.20) 21300
fse 161865 318099 732 55393 223 ( 1.03 ± 0.18) 21115
macse_p 161622 317205 1061 55715 306 (1.41 ± 0.99) 21997
needlenuc 165260 315531 2851 53613 1186 (5.49 ± 6.82) 24403
−30 −1 (71) fse0 47071 91266 230 26303 76 (1.07 ± 0.26) 12845
fse 46872 91032 233 26183 72 (1.01 ±  0.12) 12302
macse_p 46936 90876 372 26325 118 (1.66 ± 1.25) 13142
needlenuc 48290 91017 866 26135 391 (5.50 ± 5.67) 13829
−0.5 (154) fse0 120558 237768 445 37975 159 (1.03 ± 0.18) 17554
fse 120504 237678 452 37851 157 (1.01 ±  0.14) 17319
macse_p 120338 237084 691 38047 212 (1.37 ± 1.00) 17926
needlenuc 122084 236904 1321 37531 575 (3.73 ± 5.14) 18877
−0.2 (178) fse0 137451 271041 525 46049 184 (1.03 ± 0.18) 18995
fse 137440 271008 531 45917 183 (1.02 ± 0.17) 18872
macse_p 137175 270258 803 46187 244 ( 1.37 ± 0.97) 19395
needlenuc 139489 269139 1803 44303 779 (4.38 ± 6.27) 20859
  1. For varying values of the parameters fs_open_cost and fs_extend_cost, the number of CDS pairs in the dataset is given. The values of the criteria for the fse, fse0, macse_p, needlenuc methods are indicated. For each method, the average number of FS_init per alignment, with corresponding standard error values are also indicated
  2. The best results are indicated in italics