Robust Estimation of Evolutionary Distances with Information Theory

Efficient Estimation of Evolutionary Distances

The advent of high throughput sequencers has lead to a dramatic increase in the size of available genomic data. Standard methods, which have worked well for many years, are not suitable for the analysis of big data sets, due to their reliance on a time-consuming alignment step. In this thesis, a new alignment-free approach for phylogeny reconstruction is introduced. The corresponding program, a...

Estimation of evolutionary distances between homologous nucleotide sequences.

By using two models of evolutionary base substitutions--"three-substitution-type" and "two-frequency-class" models--some formulae are derived which permit a simple estimation of the evolutionary distances (and also the evolutionary rates when the divergence times are known) through comparative studies of DNA (and RNA) sequences. These formulae are applied to estimate the base substitution rates...

On the Theory of Computation and Evolutionary Distances

This paper gives a formal definition of the biological concept of evolutionary distance and an algorithm to compute it. For any set S of finite sequences of varying lengths this distance is a real-valued function on S x S, and it is shown to be a metric under conditions which are wide enough to include the biological application. The algorithm, introduced here, lends itself to computer programm...

Evolutionary Information Theory

Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary com...

Evolutionary distances