Cervus 2.0 software

The simulation takes allele frequencies either from a text file or directly from the output of the allele frequency module. These allele frequencies are used both to generate simulated genotypes and in the calculation of likelihood ratios. The simulation also takes account of the number of candidate parents, the proportion of candidate parents that are sampled, the proportion of loci typed and the proportion of loci mistyped.

It is also possible to simulate selfing and other forms of inbreeding, and to simulate candidate parents related to the true parents or offspring. By default likelihood ratios are calculated using the more powerful revised likelihood equations of Kalinowski et al.

However for comparison with previous studies it is also possible to use the original likelihood equations of Marshall et al. Following common practice in parentage testing, Cervus displays the likelihood ratio in the form of a LOD score, the natural log of the likelihood ratio. Users may select the LOD score or a derivative of it, Delta , in order to evaluate the confidence of parentage assignments. Users can select two levels of confidence for parentage assigned, relaxed and strict.

For each level of confidence the output of the simulation calculates critical values of LOD or Delta predicts the success of parentage testing using these critical values - the proportion of parentage tests expected to be resolved with this level of confidence.

Optionally users can apply the critical values from one simulation to a second simulation run with a different set of parameters. Cervus also outputs a summary of the distributions of LOD or Delta scores and provides a breakdown of parentage assignments separately for true parents and non-parents. Optionally Cervus will output the distributions of LOD or Delta, histograms of these distributions and tables of confidence levels calculated from them.

The tables can be used to determine a confidence value for each parentage assignment. In parentage analysis candidate parents or parent pairs are assigned to offspring. Cervus does the real parentage analysis in exactly the same way as the simulated parentage analysis, except using real rather than simulated genotypes. To carry out parentage analysis, Cervus needs to know the names of the offspring to be tested, the names of known parents if available and the names of the candidate parents to be tested against each offspring.

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