Quick-start examples | Simulated Data | Real Data | Background | Key Points | Mendelian Errors | Parent-pairs | Maximum mismatches | Likelihoods | Genotyping errors | Effect | Assumed genotyping error rate Err | Performance with high genotyping error rates | Effect on runtime | Error matrix | Estimate | Birth years & Ageprior | Definition & interpretation | Implementation | Smooth & Flatten | Age-based non-assignment | Parent LLR | Confidence | Low assignment rate | Causes | Remedies | Function overview | Input | Simulate | Ageprior | Pedigree reconstruction | Pedigree check | Pairwise relationships | Miscellaneous | sequoia() input | Genotypes | Subset SNPs | PLINK | Family IDs | Low call rate | Very large datasets | Birth years & sex | LifeHistData | Unknown birth years | args.AP (Customising the ageprior) | Tfilter & Tassign | Complex | Unusual relationships | Herm | UseAge | SeqList | Running sequoia() | console output | step | dams, sires | Total LL | Module | Input check | Check for duplicates | Parentage assignment | AgePrior | Full reconstruction | Dummy Individuals | Total likelihood | Save output | Output check | Pedigree stats & plots | Negative LLR's | Dyad plot | Likely relatives | Compare pedigrees | Dummy matching | Example | Colony | Relatedness | Pedigree relatedness | Genomic relatedness | Cluster families | Hermaphrodites | Herm 'A': Pedigree prior | Herm 'B': Ignore sex role | Hermaphrodite dummies | Duplicate check | Assignment errors | Parthenogenesis | FAQ | Error about/due to input data | Low assignment rate | Not enough SNPs | Too many SNPs | Genotyping errors | Lacking sex information | Insufficient age information | Uninformative age prior | Mating system | Death year | Accuracy | Field pedigree | Data simulation | Add new individuals | Results differ from COLONY | References

In short | Age Info is Useful | Implementation | Passing the threshold | Time units | Runtime Messages | Changing the ageprior | Maths | AgePrior | Unsampled individuals | Genetics $\times$ Age | AgePrior matrix explained | AgePriorExtra | Default ageprior | Pedigree-based ageprior | Discrete generations | Generation interval different from 1 | Overlapping generations | BirthYearRange | MaxAgeParent | Counts: tblA.R | P(A|R): PA.R | Full sibling correction | Ageprior P(A|R)/P(A): LR.RU.A.raw | Small sample correction | The problem | Smooth | Flatten | Weighing factor & lambdaNW | Sample size vs. sampling probability | Grandparents & Avuncular | Ageprior to Probability to Ageprior | change from v1.3 to v2.0 | Customise | Via args.AP | Different input pedigree | Other tweaks | From age-difference distribution | Specifications | Estimate birth years | References

Why use mitochondrial data | Limitations | Input | Example

Get started | Simulate genotypes | Parentage assignment | Pedigree reconstruction | Save results

Example: PedCompare | Why compare pedigrees | Study population | Comparing pedigrees | $MergedPed | id columns | $DummyMatch | $Counts | Mismatch | Mismatch Issue1: GreenBlue | Mismatch Issue2: OrangeGreen | Mismatch Issue3: YellowBlue | Mismatch Issue4: GreenYellow | Pedigree1-only | General | Griffins | Pedigree2-only (newly assigned mum) | Warning re dummy numbering