An optimal reconciliation algorithm for gene trees with polytomies

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

Volumn 7534 LNBI, Issue , 2012, Pages 106-122

  Lafond, Manuel ^a   Swenson, Krister M ^a   El Mabrouk, Nadia ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARBITRARY DEGREE; EVOLUTIONARY RELATIONSHIPS; GENE FAMILIES; GENE TREE; LINEAR-TIME ALGORITHMS; NON-BINARY; OPTIMAL ALGORITHM; RECONCILIATION ALGORITHMS; ROOTED TREES; WEAK EDGE;

BINARY TREES; BIOINFORMATICS; CLUSTERING ALGORITHMS; GENES; OPTIMIZATION;

TREES (MATHEMATICS);

EID: 84866665369     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-33122-0_9     Document Type: Conference Paper

References (22)

1. Akerborg, O., Sennblad, B., Arvestad, L., Lagergren, J.: Simultaneous bayesian gene tree reconstruction and reconciliation analysis. Proceedings of the National Academy of Sciences USA 106(14), 5714-5719 (2009)
2. Arvestad, L., Berglung, A.-C., Lagergren, J., Sennblad, B.: Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. In: Gusfield, D. (ed.) RECOMB 2004: Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology, pp. 326-335. ACM, New York (2004)
3. Chang, W.-C., Eulenstein, O.: Reconciling Gene Trees with Apparent Polytomies. In: Chen, D.Z., Lee, D.T. (eds.) COCOON 2006. LNCS, vol. 4112, pp. 235-244. Springer, Heidelberg (2006)
4. Chang, W.C., Eulenstein, O.: Reconciling gene trees with apparent polytomies, technical report. Department of Computer Science, Iowa State University (2006)
5. Chauve, C., El-Mabrouk, N.: New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. In: Batzoglou, S. (ed.) RECOMB 2009. LNCS, vol. 5541, pp. 46-58. Springer, Heidelberg (2009)
6. Chen, K., Durand, D., Farach-Colton, M.: Notung: Dating gene duplications using gene family trees. Journal of Computational Biology 7, 429-447 (2000)
7. Csu{combining double acute accent}rös, M.: Ancestral reconstruction by asymmetric wagner parsimony over continuous characteand squared parsimony over distributions. In: Sixth RECOMB Satellite Workshop on Comparative Genomics, pp. 72-86 (2008)
8. Doroftei, A., El-Mabrouk, N.: Removing Noise from Gene Trees. In: Przytycka, T.M., Sagot, M.-F. (eds.) WABI 2011. LNCS (LNBI), vol. 6833, pp. 76-91. Springer, Heidelberg (2011)
9. Doyon, J.-P., Ranwez, V., Daubin, V., Berry, V.: Models, algorithms and programs for phylogeny reconciliation. Brief Bioinform. 12, 392-400 (2011)
10. Doyon, J.-P., Scornavacca, C., Gorbunov, K.Y., Szöllo{combining double acute accent}si, G.J., Ranwez, V., Berry, V.: An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers. In: Tannier, E. (ed.) RECOMB-CG 2010. LNCS, vol. 6398, pp. 93-108. Springer, Heidelberg (2010)
11. Durand, D., Haldórsson, B.V., Vernot, B.: A hybrid micro-macroevolutionary approach to gene tree reconstruction. Journal of Computational Biology 13, 320-335 (2006)
12. Fang, G., Bhardwaj, N., Robilotto, R., Gerstein, M.B.: Getting started in gene orthology and functional analysis. PLoS Comput. Biol. 6(3), e1000703 (2010)
13. Goodman, M., Czelusniak, J., Moore, G.W., Romero-Herrera, A.E., Matsuda, G.: Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Zoology 28, 132-163 (1979)
14. Gorecki, P., Tiuryn, J.: DLS-trees: a model of evolutionary scenarios. Theoretical Computer Science 359, 378-399 (2006)
15. Hahn, M.W.: Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biology 8(R141) (2007)
16. Ma, B., Li, M., Zhang, L.: From gene trees to species trees. SIAM J. on Comput. 30, 729-752 (2000)
17. Slowinski, J.B.: Molecular polytomies. Molecular Phylogenetics and Evolution 19(1), 114-120 (2001)
18. Tofigh, A., Hallett, M., Lagergren, J.: Simultaneous identification of duplications and lateral gene transfers. IEEE/ACM Trans. Comput. Biol. Bioinform. 8, 517-535 (2011)
19. Zhang, J.: Evolution by gene duplication: an update. Trends in Ecology and Evolution 18(6), 292-298 (2003)
20. Zhang, L.X.: On Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. Journal of Computational Biology 4, 177-188 (1997)
21. Zheng, Y., Wu, T., Zhang, L.: Reconciliation of gene and species trees with polytomies, eprint arXiv:1201.3995 (2012)
22. Zmasek, C.M., Eddy, S.R.: A simple algorithm to infer gene duplication and speciiation events on a gene tree. Bioinformatics 17, 821-828 (2001)