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Items: 1 to 20 of 108

1.

Comparison of methods for estimating the nucleotide substitution matrix.

Oscamou M, McDonald D, Yap VB, Huttley GA, Lladser ME, Knight R.

BMC Bioinformatics. 2008 Dec 1;9:511. doi: 10.1186/1471-2105-9-511.

2.

Tree and rate estimation by local evaluation of heterochronous nucleotide data.

Yang Z, O'Brien JD, Zheng X, Zhu HQ, She ZS.

Bioinformatics. 2007 Jan 15;23(2):169-76.

PMID:
17110369
3.

Scoredist: a simple and robust protein sequence distance estimator.

Sonnhammer EL, Hollich V.

BMC Bioinformatics. 2005 Apr 27;6:108.

5.

CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models.

Gil M, Zanetti MS, Zoller S, Anisimova M.

Mol Biol Evol. 2013 Jun;30(6):1270-80. doi: 10.1093/molbev/mst034.

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Phylogenetic analysis using parsimony and likelihood methods.

Yang Z.

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

PMID:
8919881
9.

Nucleotide substitution models and estimation of phylogeny.

Håstad O, Björklund M.

Mol Biol Evol. 1998 Nov;15(11):1381-9.

PMID:
12572602
10.

Estimation of evolutionary distances between nucleotide sequences.

Zharkikh A.

J Mol Evol. 1994 Sep;39(3):315-29.

PMID:
7932793
11.

Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution.

Matsumoto T, Akashi H, Yang Z.

Genetics. 2015 Jul;200(3):873-90. doi: 10.1534/genetics.115.177386.

12.

Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages.

Jayaswal V, Wong TK, Robinson J, Poladian L, Jermiin LS.

Syst Biol. 2014 Sep;63(5):726-42. doi: 10.1093/sysbio/syu036.

PMID:
24927722
14.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

15.

Empirical codon substitution matrix.

Schneider A, Cannarozzi GM, Gonnet GH.

BMC Bioinformatics. 2005 Jun 1;6:134.

16.

Using MODELTEST and PAUP* to select a model of nucleotide substitution.

Posada D.

Curr Protoc Bioinformatics. 2003 Feb;Chapter 6:Unit 6.5. doi: 10.1002/0471250953.bi0605s00.

PMID:
18428705
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MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.

Mol Biol Evol. 2011 Oct;28(10):2731-9. doi: 10.1093/molbev/msr121.

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