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MBEToolbox 2.0: an enhanced version of a MATLAB toolbox for molecular biology and evolution.

Cai JJ, Smith DK, Xia X, Yuen KY.

Evol Bioinform Online. 2007 Feb 6;2:179-82.


MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.

Cai JJ, Smith DK, Xia X, Yuen KY.

BMC Bioinformatics. 2005 Mar 22;6:64.


PAML 4: phylogenetic analysis by maximum likelihood.

Yang Z.

Mol Biol Evol. 2007 Aug;24(8):1586-91. Epub 2007 May 4.


MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.

Tamura K, Dudley J, Nei M, Kumar S.

Mol Biol Evol. 2007 Aug;24(8):1596-9. Epub 2007 May 7.


Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates.

Zhang Z, Yu J.

Genomics Proteomics Bioinformatics. 2006 Aug;4(3):173-81.


Vestige: maximum likelihood phylogenetic footprinting.

Wakefield MJ, Maxwell P, Huttley GA.

BMC Bioinformatics. 2005 May 29;6:130.


GARD: a genetic algorithm for recombination detection.

Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD.

Bioinformatics. 2006 Dec 15;22(24):3096-8. Epub 2006 Nov 16.


SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB.

Schmidt H.

Bioinformatics. 2007 Mar 1;23(5):646-7. Epub 2007 Jan 18.


PGEToolbox: A Matlab toolbox for population genetics and evolution.

Cai JJ.

J Hered. 2008 Jul-Aug;99(4):438-40. doi: 10.1093/jhered/esm127. Epub 2008 Feb 29.


CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation.

Arenas M, Lopes JS, Beaumont MA, Posada D.

Mol Biol Evol. 2015 Apr;32(4):1109-12. doi: 10.1093/molbev/msu411. Epub 2015 Jan 9.


Not so different after all: a comparison of methods for detecting amino acid sites under selection.

Kosakovsky Pond SL, Frost SD.

Mol Biol Evol. 2005 May;22(5):1208-22. Epub 2005 Feb 9.


SBMLToolbox: an SBML toolbox for MATLAB users.

Keating SM, Bornstein BJ, Finney A, Hucka M.

Bioinformatics. 2006 May 15;22(10):1275-7. Epub 2006 Mar 30.


Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates.

Wang DP, Wan HL, Zhang S, Yu J.

Biol Direct. 2009 Jun 16;4:20. doi: 10.1186/1745-6150-4-20.


BEAST: Bayesian evolutionary analysis by sampling trees.

Drummond AJ, Rambaut A.

BMC Evol Biol. 2007 Nov 8;7:214.


Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes.

Holder MT, Zwickl DJ, Dessimoz C.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):4013-21. doi: 10.1098/rstb.2008.0162.


Robust inference of positive selection from recombining coding sequences.

Scheffler K, Martin DP, Seoighe C.

Bioinformatics. 2006 Oct 15;22(20):2493-9. Epub 2006 Aug 7.

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