Concatenation analyses in the presence of incomplete lineage sorting

PLoS Currents

Volumn 7, Issue TREEOFLIFE, 2015, Pages

  Warnow, Tandy ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

SPECIES; THEORETICAL MODEL;

EID: 84958559378     PISSN: None     EISSN: 21573999     Source Type: Journal    
DOI: 10.1371/currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7     Document Type: Article

References (22)

1. Roch, S. and M. Steel (2015). "Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent." Theoretical Population Biology, Volume 100, pages 56-62, 2015. [PubMed]
2. Kubatko, L.S., Degnan, J.H. (2007). "Inconsistency of phylogenetic estimates from concatenated data under coalescence." Syst. Biol. 56 (1), 17-24. [PubMed]
3. Degnan, J.H., Rosenberg, N.A. (2009). "Gene tree discordance, phylogenetic inference and the multispecies coalescent." Trends Ecol. Evol. 24 (6), 332-340. [PubMed]
4. S. Mirarab, R. Reaz, Md. S. Bayzid, T. Zimmermann, M.S. Swenson, and T. Warnow (2014). "ASTRAL: Genome-Scale Coalescent-Based Species Tree Estimation." Proceedings, ECCB (European Conference on Computational Biology), 2014. Also, Bioinformatics 2014 30 (17): i541-i548. doi: 10.1093/bioinformatics/btu462. [PMC free article] [PubMed]
5. Patel, S., R. T. Kimball, and E. L. Braun (2013). "Error in phylogenetic estimation for bushes in the tree of life." Journal of Phylogenetics and Evolutionary Biology 1:110.
6. Bayzid, M.S., Warnow, T. (2013). "Naive binning improves phylogenomic analyses." Bioinformatics 29 (18), 2277-2284. [PubMed]
7. S. Roch and T. Warnow (2015). "On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods", Systematic Biology 2015: doi: 10.1093/sysbio/syv016 [PubMed]
8. Gatesy, J., Springer, M.S. (2013). "Concatenation versus coalescence versus concatalescence." Proc. Natl. Acad. Sci. USA 110 (13), E1179. [PMC free article] [PubMed]
9. Tonini J, Moore A, Stern D, Shcheglovitova M, Ortí G. (2015). "Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated Conditions." PLOS Currents Tree of Life. 2015 Mar 9. Edition 1. doi: 10.1371/currents.tol.34260cc27551a527b124ec5f6334b6be. [PMC free article] [PubMed]
10. M. S. Bayzid, S. Mirarab, and T. Warnow (2014). "Weighted Statistical Binning: enabling statistically consistent genome-scale phylogenetic analyses", on arXiv.org: http://arxiv.org/abs/1412.5454 [PMC free article] [PubMed]
11. S. Mirarab, Md. S. Bayzid, B. Boussau, and T. Warnow (2014). "Statistical binning enables an accurate coalescent-based estimation of the avian tree". Science, 12 December 2014: 1250463. Science [PubMed]
12. Liu, L., L. Yu, and S. V. Edwards (2010). "A maximum pseudo-likelihood approach for estimating species trees under the coalescent model." BMC Evolutionary Biology 10:302. [PMC free article] [PubMed]
13. Gatesy J, Springer MS. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol Phylogenet Evol. 2014 Nov;80:231-66. PubMed PMID:25152276. [PubMed]
14. Liu, L, Z. Xi, S. Wu, C. Davis, and S. Edwards (2014), "Estimating phylogenetic trees from genome-scale data." arXiv:1501.03578v1.
15. Chifman, J. and L. Kubatko (2014). "Quartet inference from SNP data under the coalescent model." Bioinformatics 2014 Dec 1;30(23):3317-24. doi: 10.1093/bioinformatics/btu530 [PMC free article] [PubMed]
16. Chifman, J. and L. Kubatko (2014). "Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes". arXiv:1406.4811 [PubMed]
17. Liu, L., Zhenxiang Xi, Shaoyuan Wu, Charles Davis, and Scott V. Edwards. "Estimating phylogenetic trees from genome-scale data", arXiv:1501.03578
18. Mossel, E. and S. Roch. "Distance-based species tree estimation: information-theoretic trade-off between number of loci and sequence length under the coalescent". ArXiv 1504.05289v1
19. Dasarathy, G., R. Nowak and S. Roch. "Data Requirement for Phylogenetic Inference from Multiple Loci: A New Distance Method." IEEE/ACM Trans. Comput. Biol. Bioinf. 12 (2) 2015 [PubMed]
20. Heled, J. and A.J. Drummond. "Bayesian inference of species trees from multilocus data". Molecular Biology and Evolution 27 (3), 570-580 [PMC free article] [PubMed]
21. Bayzid, M.S., and T Warnow. "Naive binning improves phylogenomic analyses", Bioinformatics 29 (18), 2277-2284 [PubMed]
22. Larget, B.R., S.K. Kotha, C. N. Dewey, and C. Ané. "BUCKy: Gene Tree / Species Tree Reconciliation with Bayesian Concordance Analysis", Bioinformatics first published online September 21, 2010, doi:10.1093/bioinformatics/btq539 [PubMed]