EcceTERA: Comprehensive gene tree-species tree reconciliation using parsimony

Bioinformatics

Volumn 32, Issue 13, 2016, Pages 2056-2058

  Jacox, Edwin ^a   Chauve, Cedric ^b   Szöllosi, Gergely J ^c   Ponty, Yann ^d   Scornavacca, Celine ^a,e  

^a UNIV MONTPELLIER   (France)

^b SIMON FRASER UNIVERSITY   (Canada)

^c EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^d ÉCOLE POLYTECHNIQUE   (France)

^e LIRMM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGY; GENE DUPLICATION; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYLOGENY; PROCEDURES; THEORETICAL MODEL;

ALGORITHMS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE DUPLICATION; MODELS, THEORETICAL; MULTIGENE FAMILY; PHYLOGENY;

EID: 85007247080     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw105     Document Type: Article

References (27)

1. Bansal,M.S. et al. (2012) Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics, 28, i283-i291.
2. Bansal,M.S. et al. (2015) Improved gene tree error correction in the presence of horizontal gene transfer. Bioinformatics, 31, 1211-1218.
3. Chauve,C. et al. (2013). Duplication, rearrangement and reconciliation: A follow-up 13 years later. In: Chauve, C. et al (eds) Models and Algorithms for Genome Evolution. Springer, London, pp. 47-62.
4. Chevenet,F. et al. (2016) Sylvx: A viewer for phylogenetic tree reconciliations. Bioinformatics, 32, 608-610.
5. Conow,C. et al. (2010) Jane: A new tool for the cophylogeny reconstruction problem. Algorithms Mol. Biol., 5, 16.
6. David,L.A. and Alm,E.J. (2010) Rapid evolutionary innovation during an Archaean genetic expansion. Nature, 469, 93-96.
7. Donati,B. et al. (2015) EUCALYPT: efficient tree reconciliation enumerator. Algorithms Mol. Biol., 10, 3.
8. Doyon,J. et al. (2010) An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers. In: Comparative Genomics-International Workshop, RECOMB-CG 2010, Ottawa, Canada, October 9-11, 2010. Proceedings, volume 6398 of Lecture Notes in Computer Science, pp. 93-108. Springer.
9. Doyon,J. et al. (2011) Models, algorithms and programs for phylogeny reconciliation. Brief. Bioinf., 12, 392-400.
10. Durand,D. et al. (2006) A hybrid micro-macroevolutionary approach to gene tree reconstruction. J. Comput. Biol., 13, 320-335.
11. Goodman,M. et al. (1979) Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool., 28, 132-163.
12. Guéguen,L. et al. (2013) Bio++: efficient extensible libraries and tools for computational molecular evolution. Mol. Biol. Evol., 30, 1745-1750.
13. Hallett,M. et al. (2004) Simultaneous identification of duplications and lateral transfers. In: Proceedings of the Eight International Conference on Research in Computational Molecular Biology (RECOMB). ACM Press, pp. 347-356.
14. Nguyen,T. et al. (2012) Accounting for gene tree uncertainties improves gene trees and reconciliation inference. In: Raphael,B. and Tang,J. (eds) Algorithms in Bioinformatics, volume 7534 of Lecture Notes in Computer Science. Berlin, Heidelberg: Springer, pp. 123-134.
15. Nguyen,T.H. et al. (2013) Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods. PloS ONE, 8, e73667.
16. Ovadia,Y. et al. (2011) The cophylogeny reconstruction problem is np-complete. J. Comput. Biol., 18, 59-65.
17. Page,R.D. (1994) Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol., 43, 58-77.
18. Rusin,L.Y. et al. (2014) Reconciliation of gene and species trees. BioMed Res. Int., 2014, 642089.
19. Scornavacca,C. et al. (2013) Representing a set of reconciliations in a compact way. J. Bioinf. Comput. Biol., 11, 1250025.
20. Scornavacca,C. et al. (2015) Joint amalgamation of most parsimonious reconciled gene trees. Bioinformatics, 31, 841-848.
21. Stolzer,M. et al. (2012) Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics, 28, i409-i415.
22. Szollosi,G.J. and Daubin,V. (2012) Modeling gene family evolution and reconciling phylogenetic discord. Methods Mol. Biol., 856, 29-51.
23. Szollosi,G.J. et al. (2013a) Efficient exploration of the space of reconciled gene trees. Syst. Biol., 62, 901-912.
24. Szollosi,G.J. et al. (2013b) Lateral gene transfer from the dead. Syst. Biol., 62, 386-397.
25. Szollosi,G. et al. (2015) The inference of gene trees with species trees. Syst. Biol., 64, e42-e62.
26. To,T.H. et al. (2015) A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality. BMC Bioinf., 16, 384.
27. Tofigh,A. et al. (2011) Simultaneous identification of duplications and lateral gene transfers. IEEE/ACM Trans. Comput. Biol. Bioinf., 8, 517-535.