Table 1 The tetrad detection software applied to various simulated test sets. Three simulated datasets are shown (indicated in the column Set): Small (100 tetrads, 1000 markers), Medium (1000 tetrads, 10000 markers), and Large (1000 tetrads, 100000 markers). The first four columns of the table show the various parameters of the simulated data considered: Nt shows the number of tetrads in the set, Nm shows the number of randomly selected markers as well as the percentage of the original set of markers, and columns Noise and Missing show the amount of noise and missing values (in percent) added to the data. The software was run on these test sets with different parameters. The table shows only the parameter settings that produced the optimal result. For the results of the software with other settings see Table 4 in Appendix H. Column “Cent calling” shows whether the software estimates the recombination frequency empirically or uses its default value derived from published data (Mancera et al. 2008). The column “Sim coeff.” shows the similarity threshold being used. The columns 2:2 cutoff and 2:1 cutoff show the cutoff values for 2:2 and 2:1 segregation score for the software to call two spores sisters. The last two columns show the performance of the software, the total runtime (Intel Core i7-7820X CPU @ 3.60GHz and 64 GB RAM) and the percent of total tetrads detected by the software. Note that in all the cases when the software detected 100% of tetrads, there were no false positives. In the case when 99.8% of tetrads were detected, there was 1 false positive tetrad and 1 false positive triplet (with 1 spore unassigned)
Test set parametersSoftware parametersPerformance
SetNtNmNoise %Missing %Cent. callingSim coeff2:2 cutoff2:1 cutoffRun timeDetected tetrads %
Small100500 (50%)00yes0.210.90.956.0100%
05yes0.190.90.955.7100%
010yes0.20.90.956.2100%
50yes0.20.750.886.7100%
100yes0.240.60.838.1100%
984 (100%)00yes0.130.90.9512.9100%
05yes0.140.90.9512.3100%
010yes0.130.90.9512.1100%
50yes0.20.750.8814.3100%
100yes0.220.60.8316.0100%
Medium10001000 (10%)00no0.120.90.9502:10.2100%
05no0.110.90.9502:37.4100%
010no0.120.90.9502:27.2100%
50no0.140.750.8827:15.2100%
100no0.160.60.8314:14:47.799.80%
9984 (100%)00no0.10.90.9503:38.2100%
05no0.10.90.9504:09.1100%
010no0.090.90.9503:32.5100%
50no0.120.750.8817:35.0100%
100no0.170.60.8326:43:15.6100%
Large100010000 (10%)00no0.070.90.9503:28.3100%
05no0.120.90.9503:40.0100%
010no0.090.90.9503:35.7100%
50no0.120.750.8818:46.4100%
100no0.160.60.8331:13:42.7100%
50000 (50%)00no0.070.90.9510:45.2100%
05no0.050.90.9508:33.1100%
010no0.070.90.9510:40.6100%
50no0.120.750.8836:59.5100%
100no0.140.60.8393:53:41.7100%