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Conservation Genetics Resources

, Volume 2, Issue 1, pp 147–150 | Cite as

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

  • J. A. CoombsEmail author
  • B. H. Letcher
  • K. H. Nislow
Technical Note

Abstract

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/.

Keywords

Parentage assignment Sibship reconstruction Pedigree Genetics Accuracy Congruence 

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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Program in Organismic and Evolutionary BiologyUniversity of MassachusettsAmherstUSA
  2. 2.S.O. Conte Anadromous Fish Research Center, US Geological Survey/Leetown Science CenterTurners FallsUSA
  3. 3.Northern Research Station, US Forest ServiceUniversity of MassachusettsAmherstUSA

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