Abstract paml, currently in version 4, is a package of programs for phylogenetic analyses of
DNA and protein sequences using maximum likelihood (ML). The programs may be used to …

Natural proteins are often only slightly more stable in the native state than the denatured
state, and an increase in environmental temperature can easily shift the balance toward …

In historical biogeography, model-based inference methods for reconstructing the evolution
of geographic ranges on phylogenetic trees are poorly developed relative to the diversity of …

The reconstruction of ancestral scenarios is widely used to study the evolution of characters
along phylogenetic trees. One commonly uses the marginal posterior probabilities of the …

The field of molecular evolution has experienced explosive growth in recent years due to the
rapid accumulation of genetic sequence data, continuous improvements to computer …

Biologists frequently attempt to infer the character states at ancestral nodes of a phylogeny
from the distribution of traits observed in contemporary organisms. Because phylogenies are …

Statistical applications in fields such as bioinformatics, information retrieval, speech
processing, image processing and communications often involve large-scale models in …

Appropriate and extensive taxon sampling is one of the most important determinants of
accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary …

Testing hypotheses on drivers of clade evolution and trait diversification provides insight into
many aspects of evolutionary biology. Often, studies investigate only intrinsic biological …

Pectobacterium and Dickeya spp. are related broad-host-range entero-bacterial pathogens
of angiosperms. A review of the literature shows that these genera each cause disease in …