Grievink, Liat, Penny, David, Hendy, Mike D, Holland, Barbara R
Abstract Correction to Shavit Grievink L, Penny D, Hendy MD, Holland BR: LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites . BMC Evol...
Shavit Grievink, Liat, Penny, David, Hendy, Mike D, Holland, Barbara R
Abstract Background Commonly used phylogenetic models assume a homogeneous evolutionary process throughout the tree. It is known that these homogeneous models are often too simplistic, and that with...
Using supernetworks to distinguish hybridization from lineage-sorting (2008)
Holland, Barbara R, Benthin, Steffi, Lockhart, Peter J, Moulton, Vincent, Huber, Katharina T
Abstract Background A simple and widely used approach for detecting hybridization in phylogenies is to reconstruct gene trees from independent gene loci, and to look for gene tree incongruence....
Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution (2008)
Holland, Barbara R., Clarke, Andrew C., Meudt, Heidi M.
The amplified fragment length polymorphism (AFLP) technique is an increasingly popular component of the phylogenetic toolbox, particularly for plant species. Technological advances in capillary...
The Problem of Rooting Rapid Radiations (2007)
Shavit, Liat, Penny, David, Hendy, Michael D., Holland, Barbara R.
There are many examples of groups (such as birds, bees, mammals, multicellular animals, and flowering plants) that have undergone a rapid radiation. In such cases, where there is a combination of...
Auch, Alexander F, Henz, Stefan R, Holland, Barbara R, Göker, Markus
Abstract Background Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the...
Improved Consensus Network Techniques for Genome-Scale Phylogeny (2006)
Holland, Barbara R., Jermiin, Lars S., Moulton, Vincent
Although recent studies indicate that estimating phylogenies from alignments of concatenated genes greatly reduces the stochastic error, the potential for systematic error still remains, heightening...
Pierson, Melanie J., Martinez-Arias, Rosa, Holland, Barbara R., Gemmell, Neil J., Hurles, Matthew E., Penny, David
The settlement of the many island groups of Remote Oceania occurred relatively late in prehistory, beginning approximately 3,000 years ago when people sailed eastwards into the Pacific from Near...
Pierson, Melanie J., Martinez-Arias, Rosa, Holland, Barbara R., Gemmell, Neil J., Hurles, Matthew E., Penny, David
The settlement of the many island groups of Remote Oceania occurred relatively late in prehistory, beginning ca. 3000 years ago when people sailed eastwards into the Pacific from Near Oceania where...
Improved Consensus Network Techniques for Genome-Scale Phylogeny (2005)
Holland, Barbara R., Jermiin, Lars S., Moulton, Vincent
Although recent studies indicate that estimating phylogenies from alignments of concatenated genes greatly reduces stochastic error, the potential for systematic error still remains, heightening the...
Improved Consensus Network Techniques for Genome-Scale Phylogeny (2005)
Holland, Barbara R., Jermiin, Lars S., Moulton, Vincent
Although recent studies indicate that estimating phylogenies from alignments of concatenated genes greatly reduces stochastic error, the potential for systematic error still remains, heightening the...
Kennedy, Martyn, Holland, Barbara R., Gray, Russell D., Spencer, Hamish G.
Long-branch attraction is a well-known source of systematic error that can mislead phylogenetic methods; it is frequently invoked post hoc, upon recovering a different tree from the one expected...
Holland, Barbara R., Delsuc, Frédéric, Moulton, Vincent, Baker, Allan
Many phylogenetic methods produce large collections of trees as opposed to a single tree, which allows the exploration of support for various evolutionary hypotheses. However, to be useful, the...
Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny (2004)
Holland, Barbara R., Huber, Katharina T., Moulton, Vincent, Lockhart, Peter J.
Building species phylogenies from genome data requires the evaluation of phylogenetic evidence from independent gene loci. We propose an approach to do this using consensus networks. We compare gene...
Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny (2004)
Holland, Barbara R., Huber, Katharina T., Moulton, Vincent, Lockhart, Peter J.
Building species phylogenies from genome data requires the evaluation of phylogenetic evidence from independent gene loci. We propose an approach to do this using consensus networks. We compare gene...
Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny (2004)
Holland, Barbara R., Huber, Katharina T., Moulton, Vincent, Lockhart, Peter J.
Building species phylogenies from genome data requires the evaluation of phylogenetic evidence from independent gene loci. We propose an approach to do this using consensus networks. We compare gene...
Zhang, Ningxin, Harrex, Annette L., Holland, Barbara R., Fenton, Lauren E., Cannon, Richard D., Schmid, Jan
The ALS (agglutinin-like sequence) gene family encodes proteins that play a role in adherence of the yeast Candida albicans to endothelial and epithelial cells. The proteins are proposed as virulence...
Upper bounds on maximum likelihood for phylogenetic trees (2003)
Hendy, Michael D., Holland, Barbara R.
We introduce a mechanism for analytically deriving upper bounds on the maximum likelihood for genetic sequence data on sets of phylogenies. A simple ‘partition’ bound is introduced for general...
Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach (2000)
Chor, Benny, Hendy, Michael D., Holland, Barbara R., Penny, David
Maximum likelihood (ML) is a widely used criterion for selecting optimal evolutionary trees. However, the nature of the likelihood surface for trees is still not sufficiently understood, especially...
Zhang, Ningxin, Harrex, Annette L., Holland, Barbara R., Fenton, Lauren E., Cannon, Richard D., Schmid, Jan
The ALS (agglutinin-like sequence) gene family encodes proteins that play a role in adherence of the yeast Candida albicans to endothelial and epithelial cells. The proteins are proposed as virulence...
Zhang, Ningxin, Harrex, Annette L., Holland, Barbara R., Fenton, Lauren E., Cannon, Richard D., Schmid, Jan
The ALS (agglutinin-like sequence) gene family encodes proteins that play a role in adherence of the yeast Candida albicans to endothelial and epithelial cells. The proteins are proposed as virulence...
Optimal alphabets for an RNA world.
Gardner, Paul P, Holland, Barbara R, Moulton, Vincent, Hendy, Mike, Penny, David
Experiments have shown that the canonical AUCG genetic alphabet is not the only possible nucleotide alphabet. In this work we address the question 'is the canonical alphabet optimal?' We make the...
Using supernetworks to distinguish hybridization from lineage-sorting
Holland, Barbara R, Benthin, Steffi, Lockhart, Peter J, Moulton, Vincent, Huber, Katharina T
Grievink, Liat Shavit, Penny, David, Hendy, Mike D, Holland, Barbara R
Correction to Shavit Grievink L, Penny D, Hendy MD, Holland BR: LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evol Biol...