{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T18:20:44Z","timestamp":1768069244050,"version":"3.49.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2793,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: We present a software package for pedigree reconstruction in natural populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). If available, the algorithm makes use of prior information such as known relationships (sub-pedigrees) or the age and sex of individuals. Statistical confidence is estimated by Markov Chain Monte Carlo (MCMC) sampling. The accuracy of the algorithm is demonstrated for simulated data as well as an empirical dataset with known pedigree. The parentage inference is robust even in the presence of genotyping errors.<\/jats:p><jats:p>Availability: The C source code of FRANz can be obtained under the GPL from http:\/\/www.bioinf.uni-leipzig.de\/Software\/FRANz\/.<\/jats:p><jats:p>Contact: \u00a0markus@bioinf.uni-leipzig.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp064","type":"journal-article","created":{"date-parts":[[2009,2,9]],"date-time":"2009-02-09T01:12:42Z","timestamp":1234141962000},"page":"2134-2139","source":"Crossref","is-referenced-by-count":93,"title":["FRANz: reconstruction of wild multi-generation pedigrees"],"prefix":"10.1093","volume":"25","author":[{"given":"Markus","family":"Riester","sequence":"first","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 2RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology (IZI), Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 3Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria and 4The Santa Fe Institute, 1399 Hyde Park Road., Santa Fe, New Mexico, USA"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 2RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology (IZI), Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 3Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria and 4The Santa Fe Institute, 1399 Hyde Park Road., Santa Fe, New Mexico, USA"},{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 2RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology (IZI), Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 3Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria and 4The Santa Fe Institute, 1399 Hyde Park Road., Santa Fe, New Mexico, USA"},{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 2RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology (IZI), Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 3Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria and 4The Santa Fe Institute, 1399 Hyde Park Road., Santa Fe, New Mexico, USA"},{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 2RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology (IZI), Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 3Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria and 4The Santa Fe Institute, 1399 Hyde Park Road., Santa Fe, New Mexico, USA"}]},{"given":"Konstantin","family":"Klemm","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 2RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology (IZI), Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 3Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria and 4The Santa Fe Institute, 1399 Hyde Park Road., Santa Fe, New Mexico, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,2,8]]},"reference":[{"key":"2023013112095125000_B1","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/S0040-5809(02)00048-5","article-title":"A simulated annealing algorithm for maximum likelihood pedigree reconstruction","volume":"63","author":"Almudevar","year":"2003","journal-title":"Theor. Popul. Biol."},{"key":"2023013112095125000_B2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. Ser. B (Methodol.)"},{"key":"2023013112095125000_B3","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1093\/bioinformatics\/btm219","article-title":"Reconstructing sibling relationships in wild populations","volume":"23","author":"Berger-Wolf","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013112095125000_B4","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1016\/S0169-5347(03)00225-8","article-title":"DNA-based methods for pedigree reconstruction and kinship analysis in natural populations","volume":"18","author":"Blouin","year":"2003","journal-title":"Trends Ecol. Evol."},{"key":"2023013112095125000_B5","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1086\/514862","article-title":"Accurate inference of relationships in sib-pair linkage studies","volume":"61","author":"Boehnke","year":"1997","journal-title":"Am. J. Hum. Genet."},{"key":"2023013112095125000_B6","doi-asserted-by":"crossref","first-page":"3261","DOI":"10.1111\/j.1365-294X.2004.02346.x","article-title":"How to track and assess genotyping errors in population genetics studies","volume":"13","author":"Bonin","year":"2004","journal-title":"Mol. Ecol."},{"key":"2023013112095125000_B7","doi-asserted-by":"crossref","first-page":"1563","DOI":"10.1086\/302112","article-title":"Estimation of pairwise relationships in the presence of genotyping errors","volume":"63","author":"Broman","year":"1998","journal-title":"Am. J. Hum. Genet."},{"key":"2023013112095125000_B8","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1007\/BF00265336","article-title":"Fractional paternity assignment: theoretical development and comparison to other methods","volume":"76","author":"Devlin","year":"1988","journal-title":"Theor. Appl. Genet."},{"key":"2023013112095125000_B9","volume-title":"Statistical Yearbook 2007 for the Federal Republic of Germany.","author":"Federal Statistical Office","year":"2007"},{"key":"2023013112095125000_B10","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1046\/j.1365-294x.2000.00961.x","article-title":"Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis","volume":"9","author":"Gerber","year":"2000","journal-title":"Mol. Ecol."},{"key":"2023013112095125000_B11","doi-asserted-by":"crossref","first-page":"3715","DOI":"10.1111\/j.1365-294X.2006.03050.x","article-title":"Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework","volume":"15","author":"Hadfield","year":"2006","journal-title":"Mol. Ecol."},{"key":"2023013112095125000_B12","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1093\/bioinformatics\/17.8.754","article-title":"MRBAYES: Bayesian inference of phylogenetic trees","volume":"17","author":"Huelsenbeck","year":"2001","journal-title":"Bioinformatics"},{"key":"2023013112095125000_B13","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1016\/j.aquaculture.2005.11.026","article-title":"Development of a microsatellite DNA parentage marker suite for black tiger shrimp penaeus monodon","volume":"255","author":"Jerry","year":"2006","journal-title":"Aquaculture"},{"key":"2023013112095125000_B14","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1046\/j.1469-1809.2000.6420117.x","article-title":"Microsatellite evolution in modern humans: a comparison of two data sets from the same populations","volume":"64","author":"Jin","year":"2000","journal-title":"Ann. Hum. Genet."},{"key":"2023013112095125000_B15","doi-asserted-by":"crossref","first-page":"2511","DOI":"10.1046\/j.1365-294X.2003.01928.x","article-title":"Methods of parentage analysis in natural populations","volume":"12","author":"Jones","year":"2003","journal-title":"Mol. Ecol."},{"key":"2023013112095125000_B16","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1007\/s10592-006-9134-9","article-title":"Maximum likelihood estimation of the frequency of null alleles at microsatellite loci","volume":"7","author":"Kalinowski","year":"2006","journal-title":"Conservation Genetics"},{"key":"2023013112095125000_B17","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1111\/j.1365-294X.2007.03089.x","article-title":"Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment","volume":"16","author":"Kalinowski","year":"2007","journal-title":"Mol. Ecol."},{"key":"2023013112095125000_B18","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1126\/science.220.4598.671","article-title":"Optimization by simulated annealing","volume":"220","author":"Kirkpatrick","year":"1983","journal-title":"Science"},{"key":"2023013112095125000_B19","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1093\/bioinformatics\/btl200","article-title":"Interpreting anonymous DNA samples from mass disasters\u2013probabilistic forensic inference using genetic markers","volume":"22","author":"Lin","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112095125000_B20","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1046\/j.1365-294x.1998.00374.x","article-title":"Statistical confidence for likelihood-based paternity inference in natural populations","volume":"7","author":"Marshall","year":"1998","journal-title":"Mol. Ecol."},{"key":"2023013112095125000_B21","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1086\/285191","article-title":"Analysis of paternity within a natural population of chamaelirium luteum. ii. patterns of male reproductive success","volume":"137","author":"Meagher","year":"1991","journal-title":"Am. Nat."},{"key":"2023013112095125000_B22","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/0040-5809(86)90006-7","article-title":"The relationship between single parent and parent pair genetic likelihoods in genealogy reconstruction","volume":"29","author":"Meagher","year":"1986","journal-title":"Theor. Popul. Biol."},{"key":"2023013112095125000_B23","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1006\/tpbi.2001.1520","article-title":"A Bayesian framework for parentage analysis: the value of genetic and other biological data","volume":"59","author":"Neff","year":"2001","journal-title":"Theor. Popul. Biol."},{"key":"2023013112095125000_B24","doi-asserted-by":"crossref","first-page":"1673","DOI":"10.1093\/genetics\/157.4.1673","article-title":"Statistical approaches to paternity analysis in natural populations and applications to the North Atlantic humpback whale","volume":"157","author":"Nielsen","year":"2001","journal-title":"Genetics"},{"key":"2023013112095125000_B25","first-page":"613","article-title":"Wild pedigrees: the way forward","volume":"275","author":"Pemberton","year":"2008","journal-title":"Proc. Biol. Sci."},{"key":"2023013112095125000_B26","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1111\/j.1751-5823.2000.tb00389.x","article-title":"On the application of markov chain monte carlo methods to genetic analyses on complex pedigrees","volume":"68","author":"Sheehan","year":"2000","journal-title":"Int. Stat. Rev."},{"key":"2023013112095125000_B27","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1111\/j.1469-1809.2006.00345.x","article-title":"Structured incorporation of prior information in relationship identification problems","volume":"71","author":"Sheehan","year":"2007","journal-title":"Ann. Hum. Genet."},{"key":"2023013112095125000_B28","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1016\/j.jtbi.2005.09.026","article-title":"Reconstructing pedigrees: a combinatorial perspective","volume":"240","author":"Steel","year":"2006","journal-title":"J. Theor. Biol."},{"key":"2023013112095125000_B29","article-title":"Reconstructing pedigrees: a stochastic perspective","author":"Thatte","year":"2007","journal-title":"J. Theor. Biol"},{"key":"2023013112095125000_B30","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.1093\/genetics\/155.4.1961","article-title":"Estimating quantitative genetic parameters using sibships reconstructed from marker data","volume":"155","author":"Thomas","year":"2000","journal-title":"Genetics"},{"key":"2023013112095125000_B31","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1017\/S0016672302005669","article-title":"Sibship reconstruction in hierarchical population structures using Markov chain Monte Carlo techniques","volume":"79","author":"Thomas","year":"2002","journal-title":"Genet. Res."},{"key":"2023013112095125000_B32","doi-asserted-by":"crossref","DOI":"10.1177\/053901847601500214","article-title":"Inference of genealogical structure","volume":"15","author":"Thompson","year":"1976","journal-title":"Soc. Sci. Inform."},{"key":"2023013112095125000_B33","doi-asserted-by":"crossref","first-page":"585","DOI":"10.2307\/2531997","article-title":"Parental and sib likelihoods in genealogy reconstruction","volume":"43","author":"Thompson","year":"1987","journal-title":"Biometrics"},{"key":"2023013112095125000_B34","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1038\/sj.hdy.6800842","article-title":"Genealogy of wine grape cultivars: \u2018Pinot\u2019 is related to \u2018Syrah\u2019","volume":"97","author":"Vouillamoz","year":"2006","journal-title":"Heredity"},{"key":"2023013112095125000_B35","doi-asserted-by":"crossref","first-page":"3169","DOI":"10.1111\/j.1365-294X.2004.02298.x","article-title":"Estimating pairwise relatedness from dominant genetic markers","volume":"13","author":"Wang","year":"2004","journal-title":"Mol. Ecol."},{"key":"2023013112095125000_B36","doi-asserted-by":"crossref","first-page":"1963","DOI":"10.1093\/genetics\/166.4.1963","article-title":"Sibship reconstruction from genetic data with typing errors","volume":"166","author":"Wang","year":"2004","journal-title":"Genetics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/16\/2134\/48994156\/bioinformatics_25_16_2134.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/16\/2134\/48994156\/bioinformatics_25_16_2134.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,7]],"date-time":"2025-02-07T13:43:16Z","timestamp":1738935796000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/16\/2134\/203763"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,2,8]]},"references-count":36,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2009,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp064","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,8,15]]},"published":{"date-parts":[[2009,2,8]]}}}