Computing Distances between Evolutionary Trees

Handbook of Combinatorial Optimization Computing Distances between Evolutionary Trees

Distances Between Phylogenetic Trees: A Survey

Phylogenetic trees have been widely used in the study of evolutionary biology for representing the tree-like evolution of a collection of species. However, different data sets and different methods often lead to the construction of different phylogenetic trees for the same set of species. Therefore, comparing these trees to determine similarities or, equivalently, dissimilarities, becomes the f...

When is it safe to use an oversimplified substitution model in tree-making?

The choice of an "optimal" mathematical model for computing evolutionary distances from real sequences is not currently supported by easy-to-use software applicable to large data sets, and an investigator frequently selects one of the simplest models available. Here we study properties of the observed proportion of differences (p-distance) between sequences as an estimator of evolutionary dista...

Case Study: Visualizing Sets of Evolutionary Trees

We describe a visualization tool which allows a biologist to explore a large set of hypothetical evolutionary trees. Interacting with such a dataset allows the biologist to identify distinct hypotheses about how different species or organisms evolved, which would not have been clear from traditional analyses. Our system integrates a point-set visualization of the distribution of hypothetical tr...

Evolutionary Distance: Estimation

Estimation of evolutionary distances between protein and deoxyribonucleic acid (DNA) sequences is important for constructing phylogenetic trees, dating species’s divergences and understanding the mechanisms of evolution of genes, proteins and populations. Many estimators of evolutionary distances have been developed in the past 30 years. They are based on different models of sequence evolution ...

Reconstruction of certain phylogenetic networks from their tree-average distances.

Trees are commonly utilized to describe the evolutionary history of a collection of biological species, in which case the trees are called phylogenetic trees. Often these are reconstructed from data by making use of distances between extant species corresponding to the leaves of the tree. Because of increased recognition of the possibility of hybridization events, more attention is being given ...