L.U.St: A tool for approximated maximum likelihood supertree reconstruction

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Akanni, Wasiu A ^a,b   Creevey, Christopher J ^c   Wilkinson, Mark ^b   Pisani, Davide ^a,d  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^c ABERYSTWYTH UNIVERSITY   (United Kingdom)

^d UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

Maximum likelihood; Phylogenomics; Supertrees; Tests of two trees

Indexed keywords

FORESTRY; GENES; HIGH LEVEL LANGUAGES; MAXIMUM LIKELIHOOD; STATISTICAL TESTS;

EVOLUTIONARY TREND; HEURISTIC SEARCH; ITS APPLICATIONS; LIKELIHOOD SCORE; PHYLOGENOMICS; PLACENTAL MAMMALS; SCIENTIFIC STUDIES; SUPERTREES;

TREES (MATHEMATICS);

FORESTRY; GENES; STATISTICAL ANALYSIS;

EUTHERIA;

ALGORITHM; ANIMAL; ARTICLE; GENOMICS; HUMAN; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; GENOMICS; HUMANS; LIKELIHOOD FUNCTIONS;

EID: 84903545547     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-183     Document Type: Article

References (37)

1. Semple C, Steel M. A supertree method for rooted trees. Discret Appl Math 2000, 105:147-158.
2. Gordon AD. Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labeled leaves. J Classif 1986, 3:335-348.
3. Aho AV, Sagiv Y, Szymanski TG, Ullman JD. Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. SIAM J Comput 1981, 10:405-421.
4. Purvis A. A modification to Baum and Ragan's method for combining phylogenetic trees. Syst Biol 1995, 44:251-255.
5. Daubin V, Gouy M, Perriere G. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 2002, 12:1080-1090.
6. Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O'Connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO. Does a tree-like phylogeny only exist at the tips in the prokaryotes?. Proc R Soc Lond Ser B Biol Sci 2004, 271:2551-2558.
7. Fitzpatrick DA, Logue ME, Stajich JE, Butler G. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol 2006, 6:99.
8. Pisani D, Cotton JA, McInerney JO. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol Biol Evol 2007, 24:1752-1760.
9. Holton TA, Pisani D. Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single-and multigene families analyzed under a supertree and supermatrix paradigm. Genome Biol Evol 2010, 2:310.
10. Baum BR. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 1992, 41:3-10.
11. Ragan MA. Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol 1992, 1:53-58.
12. Wilkinson M, Cotton JA, Lapointe F-J, Pisani D. Properties of supertree methods in the consensus setting. Syst Biol 2007, 56:330-337.
13. Lapointe F-J, Wilkinson M, Bryant D. Matrix representations with parsimony or with distances: two sides of the same coin?. Syst Biol 2003, 52:865-868.
14. Gatesy J, Springer MS. A critique of matrix representation with parsimony supertrees. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life 2004, 369-388. Dordrecht: Kluwer Academic, Bininda-Emonds ORP.
15. Wilkinson M, Thorley JL, Pisani DE, Lapointe F-J, McInerney JO. Some desiderata for liberal supertrees. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life 2004, 227-246. Dordrecht: Kluwer Academic, Bininda-Emonds ORP.
16. Cotton JA, Wilkinson M. Majority-rule supertrees. Syst Biol 2007, 56:445-452.
17. Steel M, Rodrigo A. Maximum likelihood supertrees. Syst Biol 2008, 57:243-250.
18. Bryant D, Steel M. Computing the distribution of a tree metric. IEEE/ACM Trans Comput Biol Bioinform 2009, 6:420-426.
19. Akanni WA. Developing and Applying Supertree methods in Phylogenomics and Macroevolution. 2014, PhD Thesis, Department of Biology, The National University of Ireland, Maynooth. Maynooth, Ireland.
20. Robinson D, Foulds LR. Comparison of phylogenetic trees. Math Biosci 1981, 53:131-147.
21. Kishino H, Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 1989, 29:170-179.
22. Shimodaira H, Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999, 16:1114-1116.
23. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst Biol 2002, 51:492-508.
24. Shimodaira H, Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 2001, 17:1246-1247.
25. O'Leary MA, Bloch JI, Flynn JJ, Gaudin TJ, Giallombardo A, Giannini NP, Goldberg SL, Kraatz BP, Luo Z-X, Meng J. The placental mammal ancestor and the post-K-Pg radiation of placentals. Science 2013, 339:662-667.
26. McCormack JE, Faircloth BC, Crawford NG, Gowaty PA, Brumfield RT, Glenn TC. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res 2012, 22:746-754.
27. Romiguier J, Ranwez V, Delsuc F, Galtier N, Douzery EJ. Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals. Mol Biol Evol 2013, 30:2134-2144.
28. Meredith RW, Janečka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simão TL, Stadler T. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 2011, 334:521-524.
29. 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 2012, 109:14942-14947.
30. Morgan CC, Foster PG, Webb AE, Pisani D, McInerney JO, O'Connell MJ. Heterogeneous models place the root of the placental mammal phylogeny. Mol Biol Evol 2013, 30:2145-2156.
31. Cao Y, Fujiwara M, Nikaido M, Okada N, Hasegawa M. Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data. Gene 2000, 259:149-158.
32. Corneli PS, Ward RH. Mitochondrial genes and mammalian phylogenies: increasing the reliability of branch length estimation. Mol Biol Evol 2000, 17:224-234.
33. Misawa K, Nei M. Reanalysis of Murphy et al'.s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees. J Mol Evol 2003, 57:S290-S296.
34. Foster PG, Cox CJ, Embley TM. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Philos Trans R Soc Lond B Biol Sci 2009, 364:2197-2207.
35. Rota-Stabelli O, Lartillot N, Philippe H, Pisani D. Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study. Syst Biol 2013, 62:121-133.
36. Rota-Stabelli O, Campbell L, Brinkmann H, Edgecombe GD, Longhorn SJ, Peterson KJ, Pisani D, Philippe H, Telford MJ. A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata. Proc R Soc B Biol Sci 2011, 278:298-306.
37. Creevey CJ, McInerney JO. Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 2005, 21:390-392.