SibJoin: A fast heuristic for half-sibling reconstruction

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7534 LNBI, Issue , 2012, Pages 44-56

  Brown, Daniel G ^a   Dexter, Daniel ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERING APPROACH; MENDELIAN GENETICS;

BIOINFORMATICS; HEURISTIC ALGORITHMS; INFORMATION THEORY;

CLUSTERING ALGORITHMS;

EID: 84866662069     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-33122-0_4     Document Type: Conference Paper

References (18)

1. Almudevar, A., Anderson, E.: A new version of PRT software for sibling groups reconstruction with comments regarding several issues in the sibling reconstruction problem. Mol. Ecol. Resour. 12(1), 164-178 (2011)
2. Ashley, M., Caballero, I., Chaovalitwongse, W., Dasgupta, B., Govindan, P., Sheikh, S.I., Berger-Wolf, T.Y.: KINALYZER, a computer program for reconstructing sibling groups. Mol. Ecol. Resour. 9(4), 1127-1131 (2009)
3. Berger-Wolf, T.Y., DasGupta, B.: Combinatorial reconstruction of sibling relationships. In: Proceedings of CGBI 2005, pp. 3-6 (2005)
4. Bretman, A., Tregenza, T.: Measuring polyandry in wild populations: a case study using promiscuous crickets. Mol. Ecol. 14(7), 2169-2179 (2005)
5. Brown, D.G., Berger-Wolf, T.: Discovering Kinship through Small Subsets. In: Moulton, V., Singh, M. (eds.) WABI 2010. LNCS (LNBI), vol. 6293, pp. 111-123. Springer, Heidelberg (2010), http://www.springerlink.com/index/ L719361L34H0K73M.pdf
6. Chaovalitwongse, W.A., Chou, C.A., Berger-Wolf, T.Y., DasGupta, B., Sheikh, S., Ashley, M.V., Caballero, I.C.: New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers. INFORMS J. Comp. 22(2), 180-194 (2009)
7. Coombs, J.A., Letcher, B.H., Nislow, K.H.: PedAgree: software to quantify error and assess accuracy and congruence for genetically reconstructed pedigree relationships. Conserv. Genet. Resour. 2(1), 147-150 (2010)
8. Gusfield, D.: Partition-distance: A problem and class of perfect graphs arising in clustering. Info. Proc. Lett. 82(3), 159-164 (2002)
9. Isagi, Y., Kanazashi, T., Suzuki, W., Tanaka, H., Abe, T.: Highly variable pollination patterns in Magnolia obovata revealed by microsatellite paternity analysis. Int. J. Plant Sci. 165(6), 1047-1053 (2004)
10. Jones, B., Grossman, G.D.,Walsh, D.C.I., Porter, B.A., Avise, J.C., Fiumera, A.C.: Estimating Differential Reproductive Success From Nests of Related Individuals, With Application to a Study of theMottled Sculpin, Cottus bairdi. Genetics 176(4), 2427-2439 (2007)
11. Jones, O.R., Wang, J.: Molecular marker-based pedigrees for animal conservation biologists. Animal Conservation 13(1), 26-34 (2010)
12. Lin, Y., Rajan, V., Moret, B.: A Metric for Phylogenetic Trees Based on Matching. IEEE/ACM Trans. Comp. Bio and Bioinf. 9(4), 1014-1022 (2011)
13. Meilǎ, M.: Comparing Clusterings by the Variation of Information. In: Schölkopf, B., Warmuth, M.K. (eds.) COLT/Kernel 2003. LNCS (LNAI), vol. 2777, pp. 173-187. Springer, Heidelberg (2003)
14. Painter, I.: Sibship reconstruction without parental information. J. Agric. Biol. Envir. S. 2(2), 212-229 (1997)
15. Sheikh, S.I., Berger-Wolf, T.Y., Khokhar, A.A., Caballero, I.C., Ashley, M.V., Chaovalitwongse, W., Chou, C., Dasgupta, B.: Combinatorial reconstruction of half-sibling groups from microsatellite data. J. of Bioinf. Comput. Biol. 8(2), 337-356 (2010)
16. Sogard, S.M., Gilbert-Horvath, E., Anderson, E.C., Fisher, R., Berkeley, S.A., Garza, J.C.: Multiple paternity in viviparous kelp rockfish. Sebastes Atrovirens. Environ. Biol. Fishes 81(1), 7-13 (2008)
17. Wang, J.: Sibship reconstruction from genetic data with typing errors. Genetics 166(4), 1963-1979 (2004)
18. Wang, J., Santure, A.W.: Parentage and sibship inference from multilocus genotype data under polygamy. Genetics 181(4), 1579-1594 (2009)