ASTRID: Accurate species TRees from internode distances

BMC Genomics

Volumn 16, Issue , 2015, Pages 1-13

  Vachaspati, Pranjal ^a   Warnow, Tandy ^a  

^a University of Illinois at Urbana Champaign ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE SPECIES TREES FROM INTERNODE DISTANCES; ALGORITHM; ARTICLE; BIRD; COMPUTER SIMULATION; DATA ANALYSIS SOFTWARE; INTERMETHOD COMPARISON; MAMMAL; MEASUREMENT ACCURACY; MOLECULAR CLOCK; NONHUMAN; PHYLOGENETIC TREE CONSTRUCTION METHOD; SEQUENCE ALIGNMENT; SPECIES; SPECIES TREE; TAXON; GENOMICS; MOLECULAR EVOLUTION; PHYLOGENY; SPECIES DIFFERENTIATION; THEORETICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENETIC SPECIATION; GENOMICS; MODELS, THEORETICAL; PHYLOGENY;

EID: 84944723546     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-16-S10-S3     Document Type: Article

References (40)

1. Maddison W: Gene trees in species trees. Syst Biol 1997, 46(3):523-536.
2. Kingman JFC: On the genealogy of large populations. J Appl Prob 1982, 19:27, doi:10.2307/3213548.
3. Roch S, Steel M: Likelihood-based tree reconstruction on a concatenation of alignments can be statistically inconsistent. Theoretical Population Biology 2015, 100:56-62.
4. Degnan JH, Rosenberg NA: Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 2009, 24(6):332-340, doi:10.1016/j.tree.2009.01.009.
5. Liu L, Yu L, Kubatko L, Pearl DK, Edwards SV: Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol 2009, 53(1):320-328.
6. Knowles LL, Kubatko L: Estimating Species Trees: Practical and Theoretical Aspects Wiley-Blackwell, Hoboken, NJ; 2011.
7. Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T: ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 2014, 30:541-548, doi:10.1093/bioinformatics/btu462.
8. Mirarab S, Warnow T: ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 2015, 31(12):44-52[http://bioinformatics.oxfordjournals.org/content/31/12/i44.full.pdf+html], doi:10.1093/bioinformatics/btv234.
9. Heled J, Drummond AJ: Bayesian inference of species trees from multilocus data. Mol Biol Evol 2010, 27:570-580, doi:10.1093/molbev/msp274.
10. Liu L, Pearl DK: Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol 2007, 56:504-514, doi:10.1080/10635150701429982.
11. Larget BR, Kotha SK, Dewey CN, Ané C: BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 2010, 26:2910-2911, doi:10.1093/bioinformatics/btq539.0912.4472.
12. Dasarathy G, Nowak R, Roch S: Data requirement for phylogenetic inference from multiple loci: A new distance method. IEEE/ACM Trans Comp Biol Bioinformatics 2015, 12:422-432, DOI: 10.1109/TCBB.2014.2361685.
13. Liu L, Yu L, Edwards SV: A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Biol 2010, 10:302, doi:10.1186/1471-2148-10-302.
14. Liu L, Yu L: Estimating species trees from unrooted gene trees. Syst Biol 2011, 60(5):661-667, doi:10.1093/sysbio/syr027.
15. Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, RoyChoudhury A: Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol 2012, 29(8):1917-1932.
16. Liu L, Yu L, Pearl DK, Edwards SV: Estimating species phylogenies using coalescence times among sequences. Syst Biol 2009, 58(5):468-477, doi:10.1093/sysbio/syp031.
17. Kubatko L, Carstens BC, Knowles LL: STEM: Species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009, 25:971-973.
18. Chifman J, Kubatko L: Quartet inference from SNP data under the coalescent model. Bioinformatics 2014 [http://bioinformatics.oxfordjournals.org/content/early/2014/08/27/bioinformatics.btu530.full.pdf+html], doi:10.1093/bioinformatics/btu530.
19. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-425, doi: citeulike-article-id:93683.
20. Mirarab S, Bayzid MS, Boussau B, Warnow T: Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science 2014, 346(6215):1250463.
21. Robinson DF, Foulds LR: Comparison of phylogenetic trees. Math Biosci 1981, 53:131-147.
22. Mirarab S, Bayzid MS, Bossau B, Warnow T: Statistical binning improves species tree estimation in the presence of gene tree heterogeneity. Science 2014, 346(6215):1250463.
23. Bayzid MS, Mirarab S, Warnow T: Weighted statistical binning: enabling statistically consistent genome-scale phylogenetic analyses. PLOS One 2014.
24. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT: Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 2014, 346(6215):1320-1331.
25. Song S, Liu L, Edwards SV, Wu S: Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci USA 2012, 109(37):14942-14947.
26. Mallo D, Oliviera Martins L, Posada D: SimPhy: Comprehensive Simulation of Gene, Locus and Species Trees at the Genome-wide Level [https://github.com/adamallo/SimPhy].
27. Price MN, Dehal PS, Arkin AP: FastTree 2-Approximately maximumlikelihood trees for large alignments. PLoS ONE 2010, 5(3), doi:10.1371/journal.pone.0009490.
28. Criscuolo A, Gascuel O: Fast NJ-like algorithms to deal with incomplete distance matrices. BMC Bioinformatics 2008, 9:166, doi:10.1186/1471-2105-9-166.
29. Desper R, Gascuel O: Fast and accurate phylogeny minimum-evolution principle. J Comput Biol 2002, 9:687-705, doi:10.1089/106652702761034136.
30. Bayzid MS, Hunt T, Warnow T: Disk covering methods improve phylogenomic analyses. BMC Genomics 2014, 15(Suppl 6):7.
31. Mirarab S, Bayzid MS, Warnow T: Evaluating summary methods for multilocus species tree estimation in the presence of incomplete lineage sorting. Syst Biol 2014, 63.
32. Gatesy JP, Springer MS: Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol Phylog Evol 2014, 80:231-266.
33. Bayzid MS, Warnow T: Naive binning improves phylogenomic analyses. Bioinformatics 2013, 29(18):2277-84, doi:10.1093/bioinformatics/btt394.
34. Roch S, Warnow T: On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods. Syst Biol 2015, 64(4):663-676.
35. Song S, Liu L, Edwards SV, Wu S: Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci USA 2012, 109(37):14942-14947.
36. Sukumaran J, Holder MT: DendroPy: A Python library for phylogenetic computing. Bioinformatics 2010, 26(12):1569-1571.
37. Roch S: Towards extracting all phylogenetic information from matrices of evolutionary distances. Science 2010, 327(5971):1376-1379.
38. Warnow T, Moret BME, St John K: Absolute phylogeny: true trees from short sequences. Proc 12th Ann ACM/SIAM Symp Discrete Algs (SODA01) SIAM Press, Philadelphia, PA; 2001, 186-195.
39. Gronau I, Moran S, Snir S: Fast and reliable reconstruction of phylogenetic trees with indistinguishable edges. J Random Struct Algs 2012, 40(3):350-384, doi = 10.1002/rsa.20372.
40. Nakhleh L, Roshan U, St John K, Sun J, Warnow T: Designing fast converging phylogenetic methods. Bioinformatics 2001, 17(suppl 1):190-198, doi:10.1093/bioinformatics/17.suppl 1.S190.