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Items: 1 to 20 of 119

1.

Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model.

Kück P, Mayer C, Wägele JW, Misof B.

PLoS One. 2012;7(5):e36593. doi: 10.1371/journal.pone.0036593. Epub 2012 May 9. Erratum in: PLoS One. 2012;7(10):doi/10.1371/annotation/0d9fd920-c280-4753-a5a3-e19f372e852b.

5.

Success of maximum likelihood phylogeny inference in the four-taxon case.

Gaut BS, Lewis PO.

Mol Biol Evol. 1995 Jan;12(1):152-62.

PMID:
7877489
6.
9.

Multiple sequence alignment accuracy and phylogenetic inference.

Ogden TH, Rosenberg MS.

Syst Biol. 2006 Apr;55(2):314-28.

PMID:
16611602
10.
11.

Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation.

Yang Z, Goldman N, Friday A.

Mol Biol Evol. 1994 Mar;11(2):316-24.

PMID:
8170371
12.

Maximum likelihood inference of small trees in the presence of long branches.

Parks SL, Goldman N.

Syst Biol. 2014 Sep;63(5):798-811. doi: 10.1093/sysbio/syu044. Epub 2014 Jul 4.

PMID:
24996414
13.

Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks.

Schwartz RS, Mueller RL.

BMC Evol Biol. 2010 Jan 11;10:5. doi: 10.1186/1471-2148-10-5.

14.

Long-branch attraction bias and inconsistency in Bayesian phylogenetics.

Kolaczkowski B, Thornton JW.

PLoS One. 2009 Dec 9;4(12):e7891. doi: 10.1371/journal.pone.0007891. Erratum in: PLoS One. 2010;5(3). doi: 10.1371/annotation/93635f70-47d7-4876-84f5-dd568434c9ae. PLoS One. 2010;5(6). doi: 10.1371/annotation/1cd49dad-a033-4832-b2a9-610dc84e2662. PLoS One. 2010;5(3). doi: 10.1371/annotation/fb21ff39-0500-49c9-9ab3-21d924c6299d.

15.

Quartet-mapping, a generalization of the likelihood-mapping procedure.

Nieselt-Struwe K, von Haeseler A.

Mol Biol Evol. 2001 Jul;18(7):1204-19.

PMID:
11420361
16.

Phylogenetic analysis using parsimony and likelihood methods.

Yang Z.

J Mol Evol. 1996 Feb;42(2):294-307.

PMID:
8919881
17.

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.

18.

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies.

Leaché AD, Banbury BL, Felsenstein J, de Oca AN, Stamatakis A.

Syst Biol. 2015 Nov;64(6):1032-47. doi: 10.1093/sysbio/syv053. Epub 2015 Jul 29.

19.

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

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