‘apparent’: a simple and flexible R package for accurate SNP-based parentage analysis in the absence of guiding information

Table 2 Summary of results comparing the performance of ‘apparent’ to five other parentage analysis tools in identifying the pairs of parents of 15 A. arguta offspring in a population of 77 individuals

Package/Tool	Analysis with no guiding information provided				Analysis guided with 2 genotypic classes: adults vs. offspring				Citation
Package/Tool	Error I (%)	Error II (%)	Accuracy (%)	Time (min)	Error I (%)	Error II (%)	Accuracy (%)	Time (min)	Citation
apparent	0.0	0.0	100.0	18.4	0.0	0.0	100.0	3.1	–
hsphase (pogc)	31.0	5.7	17.4	0.1	31.0	5.7	17.4	0.1	Ferdosi et al. (2014) [30]
MasterBayes (MCMCped)	15.6	22.1	48.2	2.3	0.0	0.0	100.0	0.3	Hadfield et al. (2006) [27]
ParentOffspring^a	44.4	0.0	55.6	260.4	6.3	0.0	93.8	28.9	Abdel-Haleem et al. (2013) [28]
Solomon	97.7	0.9	2.3	401.4	97.5	1.0	2.6	43.1	Christie et al. (2013) [29]
Cervus	74.6	0.0	50.9	11.9	0.0	0.0	100.0	5.3	Kalinowski et al. (2007) [44]

^aThe results from ParentOffspring are approximate because the package requires an a priori declaration of parental pairs for a given set of offspring (see main text)

ISSN: 1471-2105