PedAgree: software to quantify error and assess accuracy and congruence for genetically reconstructed pedigree relationships
- 280 Downloads
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/.
KeywordsParentage assignment Sibship reconstruction Pedigree Genetics Accuracy Congruence
- Coombs JA, Letcher BH, Nislow KH (2010) PEDAGOG: software for simulating eco-evolutionary population dynamics. Mol Ecol Resour. doi: 10.1111/j.1755-0998.2009.02803.x
- Danzmann RG (1997) PROBMAX: a computer program for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny. J Hered 88:333Google Scholar
- Hedgecock D, Eichert W (1999) WHICHPARENTS (version 1.0): a windows application for determining the most likely parents of offspring using multilocus genotype data. Computer software distributed from: http://www.bml.ucdavis.edu/whichparents.html
- Valiere N (2002) GIMLET: a computer program for analysing genetic individual identification data. Mol Ecol Notes 2:377–379Google Scholar