PedAgree: software to quantify error and assess accuracy and congruence for genetically reconstructed pedigree relationships

PedAgree is software for rapid comparison of genetically reconstructed pedigrees (RP’s). Its two primary functions are (1) to assess accuracy of a RP by comparing it to a known pedigree, and (2) to measure congruence between two RP’s. The accuracy function is used to assist in determining confidence...

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Bibliographic Details
Published in:Conservation genetics resources 2010-12, Vol.2 (1), p.147-150
Main Authors: Coombs, J. A., Letcher, B. H., Nislow, K. H.
Format: Article
Language:English
Subjects:
Accuracy
Animal Genetics and Genomics
Biodiversity
Biomedical and Life Sciences
Computer programs
Conservation Biology/Ecology
Ecology
Evolutionary Biology
Life Sciences
Pedigree
Plant Genetics and Genomics
Technical Note
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Description
Summary:PedAgree is software for rapid comparison of genetically reconstructed pedigrees (RP’s). Its two primary functions are (1) to assess accuracy of a RP by comparing it to a known pedigree, and (2) to measure congruence between two RP’s. The accuracy function is used to assist in determining confidence for a RP. The congruence function is used to determine the level of agreement between two RP’s. This function determines which links within the RP’s are identical, and thus more likely to be correct. Congruence assessment between RP’s generated by sibship reconstruction (SR) and parentage assignment (PA) programs allows for implementation of the sibship constraint method. This method has been shown to increase assigned parentage accuracy by up to 53%, and to be robust to dataset characteristics that reduce conventional PA accuracies. PedAgree can compare output produced by seven SR and twelve PA programs, and is freely available for download at https://bcrc.bio.umass.edu/pedigreesoftware/ .
ISSN:1877-7252
1877-7260
DOI:10.1007/s12686-010-9202-9