Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock—A Simulation Study von Holland, B. R., Penny, D., Hendy, M. D., Sullivan, Jack

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NTRFinder: a software tool to find nested tandem repeats von Matroud, Atheer A., Hendy, M. D., Tuffley, C. P.

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Recovering evolutionary trees under a more realistic model of sequence evolution von LOCKHART, P. J, STEEL, M. A, HENDY, M. D, PENNY, D

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Reconstructing phylogeny by Quadratically Approximated Maximum Likelihood von Woodhams, M. D., Hendy, M. D.

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Can fast early rates reconcile molecular dates with the Cambrian explosion? von Bromham, L. D., Hendy, M. D.

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A Discrete Fourier Analysis for Evolutionary Trees von HENDY, M. D, PENNY, D, STEEL, M. A

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Mathematical elegance with biochemical realism: the covarion model of molecular evolution von Penny, D, McComish, B J, Charleston, M A, Hendy, M D

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The power of relative rates tests depends on the data von Bromham, L, Penny, D, Rambaut, A, Hendy, M D

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A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction von EDVARDSSON, Sverker, GARDNER, Paul P, POOLE, Anthony M, HENDY, Michael D, PENNY, David, MOULTON, Vincent

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A fast and simple algorithm for finding the modes of a multinomial distribution von White, W.T.J., Hendy, M.D.

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Multiple maxima of likelihood in phylogenetic trees: an analytic approach von Chor, B, Hendy, M D, Holland, B R, Penny, D

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An Algorithm for Constructing Local Regions in a Phylogenetic Network von Huber, K.T., Watson, E.E., Hendy, M.D.

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The vertex-cover polynomial of a graph von DONG, F. M, HENDY, M. D, TEO, K. L, LITTLE, C. H. C

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Non-chordal graphs having integral-root chromatic polynomials II von Dong, F.M., Teo, K.L., Koh, K.M., Hendy, M.D.

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Mammalian Evolution: Timing and Implications from Using the LogDeterminant Transform for Proteins of Differing Amino Acid Composition von Penny, David, Hasegawa, Masami, Waddell, Peter J., Hendy, Michael D., Olmstead, R.

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Branch and bound algorithms to determine minimal evolutionary trees von Hendy, M.D., Penny, David

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Estimating times of divergence with a change of rate: the orangutan/African ape divergence von Penny, D, Murray-McIntosh, R P, Hendy, M D

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Toward Resolving Deep Neoaves Phylogeny: Data, Signal Enhancement, and Priors von Pratt, Renae C., Gibb, Gillian C., Morgan-Richards, Mary, Phillips, Matthew J., Hendy, Michael D., Penny, David

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Controversy on chloroplast origins von Lockhart, Peter J., Penny, David, Hendy, Michael D., Howe, Christopher J., Beanland, Timothy J., Larkum, Anthony W.D.

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Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences von Penny, D, Foulds, L.R, Hendy, M.D

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