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Volumn 12, Issue 1, 2012, Pages 164-178

A new version of PRT software for sibling groups reconstruction with comments regarding several issues in the sibling reconstruction problem

Author keywords

Pedigree reconstruction; Sibling group inference

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; ATLANTIC SALMON; BIOLOGICAL MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; GENETICS; HUMAN; MEDICAL GENETICS; PEDIGREE; SIBLING;

EID: 83955162916     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2011.03061.x     Document Type: Article
Times cited : (19)

References (42)
  • 1
    • 0034862959 scopus 로고    scopus 로고
    • A bootstrap assessment of variability in pedigree reconstruction based on DNA markers
    • Almudevar A (2001a) A bootstrap assessment of variability in pedigree reconstruction based on DNA markers. Biometrics, 57, 757-763.
    • (2001) Biometrics , vol.57 , pp. 757-763
    • Almudevar, A.1
  • 2
    • 0035180965 scopus 로고    scopus 로고
    • Most powerful permutation invariant tests for relatedness hypotheses using genotypic data
    • Almudevar A (2001b) Most powerful permutation invariant tests for relatedness hypotheses using genotypic data. Biometrics, 57, 1080-1088.
    • (2001) Biometrics , vol.57 , pp. 1080-1088
    • Almudevar, A.1
  • 3
    • 0038620466 scopus 로고    scopus 로고
    • A simulated annealing algorithm for maximum likelihood pedigree reconstruction
    • Almudevar A (2003) A simulated annealing algorithm for maximum likelihood pedigree reconstruction. Theoretical Population Biology, 63, 63-75.
    • (2003) Theoretical Population Biology , vol.63 , pp. 63-75
    • Almudevar, A.1
  • 4
    • 33846596160 scopus 로고    scopus 로고
    • A graphical approach to relatedness inference
    • Almudevar A (2007) A graphical approach to relatedness inference. Theoretical Population Biology, 71, 213-229.
    • (2007) Theoretical Population Biology , vol.71 , pp. 213-229
    • Almudevar, A.1
  • 5
    • 83955161165 scopus 로고    scopus 로고
    • A commentary on some recent methods in sibling group reconstruction based on set coverings
    • Almudevar A (2011) A commentary on some recent methods in sibling group reconstruction based on set coverings. Optimization Methods & Software, doi:.
    • (2011) Optimization Methods & Software
    • Almudevar, A.1
  • 9
    • 34547852255 scopus 로고    scopus 로고
    • Reconstructing sibling relationships in wild populations
    • Berger-Wolf TY, Sheikh SI, DasGupta B et al. (2007) Reconstructing sibling relationships in wild populations. Bioinformatics, 23, 49-56.
    • (2007) Bioinformatics , vol.23 , pp. 49-56
    • Berger-Wolf, T.Y.1    Sheikh, S.I.2    DasGupta, B.3
  • 10
    • 0141790880 scopus 로고    scopus 로고
    • DNA-based methods for pedigree reconstruction and kinship analysis in natural populations
    • Blouin MS (2003) DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends in Ecology & Evolution, 18, 503-511.
    • (2003) Trends in Ecology & Evolution , vol.18 , pp. 503-511
    • Blouin, M.S.1
  • 11
    • 2542424932 scopus 로고    scopus 로고
    • Accuracy, efficiency and robustness of four algorithms allowing full sibship reconstruction from DNA marker data
    • Butler K, Field C, Herbinger CM, Smith BR (2004) Accuracy, efficiency and robustness of four algorithms allowing full sibship reconstruction from DNA marker data. Molecular Ecology, 13, 1589-1600.
    • (2004) Molecular Ecology , vol.13 , pp. 1589-1600
    • Butler, K.1    Field, C.2    Herbinger, C.M.3    Smith, B.R.4
  • 13
    • 77952042147 scopus 로고    scopus 로고
    • New optimization model and algorithm for sibling reconstruction from genetic markers
    • Chaovalitwongse A, Chou CA, Berger-Wolf TY et al. (2010) New optimization model and algorithm for sibling reconstruction from genetic markers. INFORMS Journal on Computing, 22, 180-194.
    • (2010) INFORMS Journal on Computing , vol.22 , pp. 180-194
    • Chaovalitwongse, A.1    Chou, C.A.2    Berger-Wolf, T.Y.3
  • 14
    • 79952420122 scopus 로고    scopus 로고
    • Who are the missing parents? Grandparentage analysis identifies multiple sources of gene flow into a wild population
    • Christie MR, Marine ML, Blouin MS (2011) Who are the missing parents? Grandparentage analysis identifies multiple sources of gene flow into a wild population. Molecular Ecology, 20, 1263-1276.
    • (2011) Molecular Ecology , vol.20 , pp. 1263-1276
    • Christie, M.R.1    Marine, M.L.2    Blouin, M.S.3
  • 15
    • 43949123556 scopus 로고    scopus 로고
    • CREATE: a software to create input files from diploid genotypic data for 52 genetic software programs
    • Coombs JA, Letcher BH, Nislow KH (2008) CREATE: a software to create input files from diploid genotypic data for 52 genetic software programs. Molecular Ecology Resources, 8, 578-580.
    • (2008) Molecular Ecology Resources , vol.8 , pp. 578-580
    • Coombs, J.A.1    Letcher, B.H.2    Nislow, K.H.3
  • 16
    • 84859997108 scopus 로고    scopus 로고
    • PedAgree: software to quantify error and assess accuracy and congruence for genetically reconstructed pedigree relationships
    • Coombs JA, Letcher BH, Nislow KH (2010) PedAgree: software to quantify error and assess accuracy and congruence for genetically reconstructed pedigree relationships. Conservation Genetics Resources, 2, 147-150.
    • (2010) Conservation Genetics Resources , vol.2 , pp. 147-150
    • Coombs, J.A.1    Letcher, B.H.2    Nislow, K.H.3
  • 17
    • 0000616384 scopus 로고
    • Fractional paternity assignment: theoretical development and comparison to other methods
    • Devlin B, Roeder K, Ellstrand NC (1988) Fractional paternity assignment: theoretical development and comparison to other methods. TAG. Theoretical and Applied Genetics, 76, 369-380.
    • (1988) TAG. Theoretical and Applied Genetics , vol.76 , pp. 369-380
    • Devlin, B.1    Roeder, K.2    Ellstrand, N.C.3
  • 18
    • 0035019565 scopus 로고    scopus 로고
    • Assignment of paternity groups without access to parental genotypes: multiple mating and developmental plasticity in squid
    • Emery AM, Wilson IJ, Craig S, Boyle PR, Noble LR (2001) Assignment of paternity groups without access to parental genotypes: multiple mating and developmental plasticity in squid. Molecular Ecology, 10, 1265-1278.
    • (2001) Molecular Ecology , vol.10 , pp. 1265-1278
    • Emery, A.M.1    Wilson, I.J.2    Craig, S.3    Boyle, P.R.4    Noble, L.R.5
  • 19
    • 0002803813 scopus 로고
    • Multiple maternity and paternity in single broods of apparently monogamous eastern bluebirds Sialia sialis
    • Gowaty PA, Karlin AA (1984) Multiple maternity and paternity in single broods of apparently monogamous eastern bluebirds Sialia sialis. Behavioral Ecology and Sociobiology, 15, 91-95.
    • (1984) Behavioral Ecology and Sociobiology , vol.15 , pp. 91-95
    • Gowaty, P.A.1    Karlin, A.A.2
  • 20
    • 0037118191 scopus 로고    scopus 로고
    • Partition-distance: a problem and class of perfect graphs arising in clustering
    • Gusfield D (2002) Partition-distance: a problem and class of perfect graphs arising in clustering. Information Processing Letters, 82, 159-164.
    • (2002) Information Processing Letters , vol.82 , pp. 159-164
    • Gusfield, D.1
  • 21
    • 0030617749 scopus 로고    scopus 로고
    • Family relationships and effective population size in a natural cohort of Atlantic cod (Gadus morhua) larvae
    • Herbinger C, Doyle RW, Taggart CT et al. (1997) Family relationships and effective population size in a natural cohort of Atlantic cod (Gadus morhua) larvae. Canadian Journal of Fisheries and Aquatic Sciences, 54, 11-18.
    • (1997) Canadian Journal of Fisheries and Aquatic Sciences , vol.54 , pp. 11-18
    • Herbinger, C.1    Doyle, R.W.2    Taggart, C.T.3
  • 22
    • 0033616665 scopus 로고    scopus 로고
    • Early growth performance of Atlantic salmon full-sib families reared in single family tanks or in mixed family tanks
    • Herbinger C, O'Reilly PT, Doyle RW, Wright JM, O'Flynn F (1999) Early growth performance of Atlantic salmon full-sib families reared in single family tanks or in mixed family tanks. Aquaculture, 173, 105-116.
    • (1999) Aquaculture , vol.173 , pp. 105-116
    • Herbinger, C.1    O'Reilly, P.T.2    Doyle, R.W.3    Wright, J.M.4    O'Flynn, F.5
  • 23
    • 0141724877 scopus 로고    scopus 로고
    • Methods of parentage analysis in natural populations
    • Jones AG, Ardren WR (2003) Methods of parentage analysis in natural populations. Molecular Ecology, 12, 2511-2523.
    • (2003) Molecular Ecology , vol.12 , pp. 2511-2523
    • Jones, A.G.1    Ardren, W.R.2
  • 25
    • 34548437626 scopus 로고    scopus 로고
    • Estimating differential reproductive success from nests of related individuals, with application to a study of the mottled sculpin, Cottus bairdi
    • Jones B, Grossman GD, Walsh DC, Porter BA, Avise JC, Fiumera AC (2007) Estimating differential reproductive success from nests of related individuals, with application to a study of the mottled sculpin, Cottus bairdi. Genetics, 176, 2427-2439.
    • (2007) Genetics , vol.176 , pp. 2427-2439
    • Jones, B.1    Grossman, G.D.2    Walsh, D.C.3    Porter, B.A.4    Avise, J.C.5    Fiumera, A.C.6
  • 26
    • 75649106875 scopus 로고    scopus 로고
    • Molecular marker-based pedigrees for animal conservation biologists
    • Jones OR, Wang J (2010) Molecular marker-based pedigrees for animal conservation biologists. Animal Conservation, 13, 26-34.
    • (2010) Animal Conservation , vol.13 , pp. 26-34
    • Jones, O.R.1    Wang, J.2
  • 27
    • 27544494125 scopus 로고    scopus 로고
    • Modified SIMPSON O(n3) algorithm for the full sibship reconstruction problem
    • Konovalov DA, Bajema N, Litow B (2005a) Modified SIMPSON O(n3) algorithm for the full sibship reconstruction problem. Bioinformatics, 21, 3912-3917.
    • (2005) Bioinformatics , vol.21 , pp. 3912-3917
    • Konovalov, D.A.1    Bajema, N.2    Litow, B.3
  • 28
    • 19544375993 scopus 로고    scopus 로고
    • Partition-distance via the assignment problem
    • Konovalov DA, Litow B, Bajema N (2005b) Partition-distance via the assignment problem. Bioinformatics, 21, 2463-2468.
    • (2005) Bioinformatics , vol.21 , pp. 2463-2468
    • Konovalov, D.A.1    Litow, B.2    Bajema, N.3
  • 29
    • 9644303027 scopus 로고    scopus 로고
    • KINGROUP: a program for pedigree relationship reconstruction and kin group assignments using genetic markers
    • Konovalov DA, Manning C, Henshaw MT (2004) KINGROUP: a program for pedigree relationship reconstruction and kin group assignments using genetic markers. Molecular Ecology Notes, 4, 779-782.
    • (2004) Molecular Ecology Notes , vol.4 , pp. 779-782
    • Konovalov, D.A.1    Manning, C.2    Henshaw, M.T.3
  • 30
    • 0034748377 scopus 로고    scopus 로고
    • Parentage and grandparentage assignment with known and unknown matings: application to Connecticut River Atlantic salmon restoration
    • Letcher BH, King TL (2001) Parentage and grandparentage assignment with known and unknown matings: application to Connecticut River Atlantic salmon restoration. Canadian Journal of Fisheries and Aquatic Sciences, 58, 1812-1821.
    • (2001) Canadian Journal of Fisheries and Aquatic Sciences , vol.58 , pp. 1812-1821
    • Letcher, B.H.1    King, T.L.2
  • 31
    • 0032077236 scopus 로고    scopus 로고
    • Statistical confidence for likelihood-based paternity inference in natural populations
    • Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology, 7, 639-655.
    • (1998) Molecular Ecology , vol.7 , pp. 639-655
    • Marshall, T.C.1    Slate, J.2    Kruuk, L.E.B.3    Pemberton, J.M.4
  • 32
    • 0023480256 scopus 로고
    • Analysis of parentage for naturally established seedlings within a population of Chamaelirium luteum (Liliaceae)
    • Meagher TR, Thompson EA (1987) Analysis of parentage for naturally established seedlings within a population of Chamaelirium luteum (Liliaceae). Ecology, 68, 803-812.
    • (1987) Ecology , vol.68 , pp. 803-812
    • Meagher, T.R.1    Thompson, E.A.2
  • 34
    • 0035044518 scopus 로고    scopus 로고
    • Statistical approaches to paternity analysis in natural populations and applications to the North Atlantic humpback whale
    • Nielsen R, Mattila DK, Clapham PJ, Palsbøll PJ (2001) Statistical approaches to paternity analysis in natural populations and applications to the North Atlantic humpback whale. Genetics, 157, 1673-1682.
    • (2001) Genetics , vol.157 , pp. 1673-1682
    • Nielsen, R.1    Mattila, D.K.2    Clapham, P.J.3    Palsbøll, P.J.4
  • 35
    • 0031756017 scopus 로고    scopus 로고
    • Analysis of parentage determination in Atlantic salmon (Salmo salar) using microsatellites
    • O'Reilly PT, Herbinger C, Wright JM (1998) Analysis of parentage determination in Atlantic salmon (Salmo salar) using microsatellites. Animal Genetics, 29, 363-370.
    • (1998) Animal Genetics , vol.29 , pp. 363-370
    • O'Reilly, P.T.1    Herbinger, C.2    Wright, J.M.3
  • 37
    • 66149180574 scopus 로고    scopus 로고
    • Consensus methods for reconstruction of sibling relationships from genetic data. In: Proceedings of the 4th Multidisciplinary Workshop on Advances in Preference Handling at AAAI 08
    • Sheikh SI, Berger-Wolf TY, Khokhar AA, DasGupta B (2008) Consensus methods for reconstruction of sibling relationships from genetic data. In: Proceedings of the 4th Multidisciplinary Workshop on Advances in Preference Handling at AAAI 08, pp. 97-102.
    • (2008) , pp. 97-102
    • Sheikh, S.I.1    Berger-Wolf, T.Y.2    Khokhar, A.A.3    DasGupta, B.4
  • 38
    • 0033886119 scopus 로고    scopus 로고
    • Estimating quantitative genetic parameters using sibships reconstructed from marker data
    • Thomas SC, Hill WG (2000) Estimating quantitative genetic parameters using sibships reconstructed from marker data. Genetics, 155, 1961-1972.
    • (2000) Genetics , vol.155 , pp. 1961-1972
    • Thomas, S.C.1    Hill, W.G.2
  • 39
    • 0016558105 scopus 로고
    • The estimation of pairwise relationships
    • Thompson EA (1975) The estimation of pairwise relationships. Annals of Human Genetics, 39, 173-188.
    • (1975) Annals of Human Genetics , vol.39 , pp. 173-188
    • Thompson, E.A.1
  • 40
    • 31344435688 scopus 로고    scopus 로고
    • Bayesian approach for the genetic tracking of cultured and released individuals
    • Tringali MD (2006) Bayesian approach for the genetic tracking of cultured and released individuals. Fisheries Research, 77, 159-172.
    • (2006) Fisheries Research , vol.77 , pp. 159-172
    • Tringali, M.D.1
  • 41
    • 65549135685 scopus 로고    scopus 로고
    • Parentage and sibship inference from multilocus genotype data under polygamy
    • Wang J, Santure A (2009) Parentage and sibship inference from multilocus genotype data under polygamy. Genetics, 181, 1579-1594.
    • (2009) Genetics , vol.181 , pp. 1579-1594
    • Wang, J.1    Santure, A.2
  • 42
    • 2442544496 scopus 로고    scopus 로고
    • Sibship reconstruction from genetic data with typing errors
    • Wang JL (2004) Sibship reconstruction from genetic data with typing errors. Genetics, 166, 1963-1979.
    • (2004) Genetics , vol.166 , pp. 1963-1979
    • Wang, J.L.1


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