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Results: 1 to 20 of 133

1.

Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes.

Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O.

Syst Biol. 2011 Oct;60(5):685-99. doi: 10.1093/sysbio/syr041. Epub 2011 May 3.

PMID:
21540409
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative.

Anisimova M, Gascuel O.

Syst Biol. 2006 Aug;55(4):539-52.

PMID:
16785212
[PubMed - indexed for MEDLINE]
3.
4.

Divergent maximum-likelihood-branch-support values for polytomies.

Simmons MP, Norton AP.

Mol Phylogenet Evol. 2014 Apr;73:87-96. doi: 10.1016/j.ympev.2014.01.018. Epub 2014 Feb 4.

PMID:
24503481
[PubMed - indexed for MEDLINE]
5.

Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability.

Douady CJ, Delsuc F, Boucher Y, Doolittle WF, Douzery EJ.

Mol Biol Evol. 2003 Feb;20(2):248-54.

PMID:
12598692
[PubMed - indexed for MEDLINE]
Free Article
6.

Ultrafast approximation for phylogenetic bootstrap.

Minh BQ, Nguyen MA, von Haeseler A.

Mol Biol Evol. 2013 May;30(5):1188-95. doi: 10.1093/molbev/mst024. Epub 2013 Feb 15.

PMID:
23418397
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Measures of clade confidence do not correlate with accuracy of phylogenetic trees.

Hall BG, Salipante SJ.

PLoS Comput Biol. 2007 Mar 16;3(3):e51. Retraction in: Hall BG, Salipante SJ. PLoS Comput Biol. 2007 Jul;3(7):e158.

PMID:
17367204
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Branch-length prior influences Bayesian posterior probability of phylogeny.

Yang Z, Rannala B.

Syst Biol. 2005 Jun;54(3):455-70.

PMID:
16012111
[PubMed - indexed for MEDLINE]
9.

Model misspecification and probabilistic tests of topology: evidence from empirical data sets.

Buckley TR.

Syst Biol. 2002 Jun;51(3):509-23.

PMID:
12079647
[PubMed - indexed for MEDLINE]
10.

Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics.

Erixon P, Svennblad B, Britton T, Oxelman B.

Syst Biol. 2003 Oct;52(5):665-73.

PMID:
14530133
[PubMed - indexed for MEDLINE]
11.

SuperTRI: A new approach based on branch support analyses of multiple independent data sets for assessing reliability of phylogenetic inferences.

Ropiquet A, Li B, Hassanin A.

C R Biol. 2009 Sep;332(9):832-47. doi: 10.1016/j.crvi.2009.05.001. Epub 2009 Jun 18.

PMID:
19748458
[PubMed - indexed for MEDLINE]
12.

Assessment of substitution model adequacy using frequentist and Bayesian methods.

Ripplinger J, Sullivan J.

Mol Biol Evol. 2010 Dec;27(12):2790-803. doi: 10.1093/molbev/msq168. Epub 2010 Jul 8.

PMID:
20616145
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Bayesian model adequacy and choice in phylogenetics.

Bollback JP.

Mol Biol Evol. 2002 Jul;19(7):1171-80.

PMID:
12082136
[PubMed - indexed for MEDLINE]
Free Article
14.

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O.

Syst Biol. 2010 May;59(3):307-21. doi: 10.1093/sysbio/syq010. Epub 2010 Mar 29.

PMID:
20525638
[PubMed - indexed for MEDLINE]
15.

Does choice in model selection affect maximum likelihood analysis?

Ripplinger J, Sullivan J.

Syst Biol. 2008 Feb;57(1):76-85. doi: 10.1080/10635150801898920.

PMID:
18275003
[PubMed - indexed for MEDLINE]
16.

Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data.

Waddell PJ, Kishino H, Ota R.

Genome Inform. 2002;13:82-92.

PMID:
14571377
[PubMed - indexed for MEDLINE]
17.

Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics.

Suzuki Y, Glazko GV, Nei M.

Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16138-43. Epub 2002 Nov 25.

PMID:
12451182
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.

Zhang J, Nielsen R, Yang Z.

Mol Biol Evol. 2005 Dec;22(12):2472-9. Epub 2005 Aug 17.

PMID:
16107592
[PubMed - indexed for MEDLINE]
Free Article
19.

Phylogeographic analysis of the cornsnake (Elaphe guttata) complex as inferred from maximum likelihood and Bayesian analyses.

Burbrink FT.

Mol Phylogenet Evol. 2002 Dec;25(3):465-76.

PMID:
12450751
[PubMed - indexed for MEDLINE]
20.

Calculating the evolutionary rates of different genes: a fast, accurate estimator with applications to maximum likelihood phylogenetic analysis.

Bevan RB, Lang BF, Bryant D.

Syst Biol. 2005 Dec;54(6):900-15.

PMID:
16282169
[PubMed - indexed for MEDLINE]
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