Joint amalgamation of most parsimonious reconciled gene trees

Bioinformatics

Volumn 31, Issue 6, 2015, Pages 841-848

  Scornavacca, Celine ^a,b   Jacox, Edwin ^a   Szöllosi, Gergely J ^c  

^a CNRS   (France)

^b LIRMM   (France)

^c EÖTVÖS LORÁND UNIVERSITY   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

CYANOBACTERIA;

ALGORITHM; BACTERIAL GENOME; CLASSIFICATION; COMPUTER SIMULATION; CYANOBACTERIUM; GENE DUPLICATION; GENETICS; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYLOGENY;

ALGORITHMS; COMPUTER SIMULATION; CYANOBACTERIA; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, BACTERIAL; MULTIGENE FAMILY; PHYLOGENY;

EID: 84925250621     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu728     Document Type: Article

References (36)

1. Akerborg, O. et al. (2009). Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc. Nat. Acad. Sci. USA, 106, 5714-5719.
2. Arvestad, L. (2003). Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics, 19, 7i-15i.
3. Bansal, M.S. et al. (2012). Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics, 28, i283-i291.
4. Boussau, B. et al. (2013). Genome-scale coestimation of species and gene trees. Genome Res. 23, 323-330.
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. Doyon, J. et al. (2011). Models, algorithms and programs for phylogeny reconciliation. Brief Bioinform. 12, 392-400.
8. Doyon, J.-P. et al. (2010). An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers. In: Proceedings of the 2010 International Conference on Comparative Genomics, RECOMB-CG'10, Springer-Verlag, Berlin, Heidelberg, pp. 93-108.
9. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376.
10. Guindon, S. et al. (2010). New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321.
11. Hallett, M.T. and Lagergren, J. (2001). Efficient algorithms for lateral gene transfer problems. In: Proceedings of the Fifth Annual International Conference on Computational Biology, ACM, New York, NY, pp. 149-156.
12. Höhna, S. and Drummond, A. (2012). Guided tree topology proposals for Bayesian phylogenetic inference. Syst. Biol. 61, 1-11.
13. Larget, B. (2013). The estimation of tree posterior probabilities using conditional clade probability distributions. Syst. Biol. 62, 501-511.
14. Lartillot, N. et al. (2009). PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics, 25, 2286.
15. Le, S.Q. and Gascuel, O. (2008). An improved general amino acid replacement matrix. Mol. Biol. Evol. 25, 1307-1320.
16. Maddison, W.P. (1997). Gene trees in species trees. Syst. Biol. 46, 523-536.
17. Nguyen, T. et al. (2012). Accounting for gene tree uncertainties improves gene trees and reconciliation inference. In: B., Raphael and J Tang (eds.) Algorithms in Bioinformatics, volume 7534 of Lecture Notes in Computer Science. Springer, Berlin Heidelberg, pp. 123-134.
18. Nguyen, T.H. et al. (2013). Reconciliation and local gene tree rearrangement can be of mutual profit. Algorithms Mol Biol, 8, 12.
19. Penel, S. et al. (2009). Databases of homologous gene families for comparative genomics. BMC Bioinformatics, 6, S3.
20. Rannala, B. and Yang, Z. (2003). Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics, 164, 1645-1656.
21. Rasmussen, M.D. and Kellis, M. (2007). Accurate gene-tree reconstruction by learning gene-and species-specific substitution rates across multiple complete genomes. Genome Res. 17, 1932-1942.
22. Rasmussen, M.D. and Kellis, M. (2010). A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction. Mol. Biol. Evol. 28, 273-290.
23. Rasmussen, M.D. and Kellis, M. (2012). Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Res. 22, 755-765.
24. Ronquist, F. et al. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539-542.
25. Sjö strand, J. et al. (2014). A bayesian method for analyzing lateral gene transfer. Syst. Biol. 63, 409-420.
26. Suchard, M.A. (2005). Stochastic models for horizontal gene transfer: taking a random walk through tree space. Genetics, 170, 419-431.
27. Szö llosi, G.J. and Daubin, V. (2012). Modeling gene family evolution and reconciling phylogenetic discord. Methods Mol. Biol. 856, 29-51.
28. Szöllosi, G.J. et al. (2012). Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proc. Nat. Acad. Sci. USA, 109, 17513-17518.
29. Szöllosi, G.J. et al. (2013a). lateral gene transfer from the dead. Syst. Biol., 62, 386-397.
30. Szöllosi, G.J. et al. (2013b). Efficient exploration of the space of reconciled gene trees. Syst. Biol. 62, 901-912.
31. Szöllosi, G. et al. (2014). The inference of gene trees with species trees. Syst. Biol. 64, e42-e62.
32. Than, C. and Nakhleh, L. (2009). Species tree inference by minimizing deep coalescences. PLoS Comput. Biol. 5, e1000501.
33. Tofigh, A. (2009). Using trees to capture reticulate evolution, lateral gene transfers and cancer progression. PhD Thesis, KTH Royal Institute of Technology, Sweden.
34. Tofigh, A. et al. (2011). Simultaneous identification of duplications and lateral gene transfers. IEEE/ACM Trans. Comput. Biol. Bioinform. 8, 517-535.
35. Wu, Y.-C. et al. (2013). TreeFix: statistically informed gene tree error correction using species trees. Syst. Biol. 62, 110-120.
36. Wu, Y.-C. et al. (2014). Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees. Genome Res. 24, 475-486.