Phylogenetic profiling involves the comparison of phylogenetic data across gene families. It is possible to construct phylogenetic trees, or related data structures, for specific gene families using a wide variety of tools and approaches. Phylogenetic profiling involves the comparison of this data to determine which families have correlated or coupled evolution. The underlying assumption is tha...

All organisms have evolved from a common ancestor. The distance between these species is measured using phylogenetic analysis. It enables us to extract evolutionary relationship from sequence analysis. These relationships are depicted on phylogenetic trees. This article provides a detailed survey on different sequential approaches of sequential alignment, clustering and complete details of how ...

This paper presents the main steps to reconstruct phylogenetic trees using an evolutionary algorithm with a wide range of alternative computational procedures for fitness evaluation and for tuning the search engine. Due to the fine equilibrium between exploration and exploitation of the search space, highquality reconstructions are obtained among an explosion of candidates and with the addition...

The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale ...

Interspecific comparison has a long and productive history in physiology. Conceptual and statistical advances over the last 15 years have demonstrated several ways in which comparisons can be enhanced by consideration of phylogenetic information, i.e., empirical estimates of the ways in which organisms are related (evolutionary trees). Choice of species to be compared should be informed by phyl...

MOTIVATION Phylogenomics integrates the vast amount of phylogenetic information contained in complete genome sequences, and is rapidly becoming the standard for reliably inferring species phylogenies. There are, however, fundamental differences between the ways in which phylogenomic approaches like gene content, superalignment, superdistance and supertree integrate the phylogenetic information ...

With the exception of Bayesian analysis, phylogenetic inference procedures typically identify a best estimate of phylogenetic relationships, a so called point estimate of the phylogeny. However, the point estimate is often relatively uninteresting in itself unless we have some measure of its reliability. This lecture will be about techniques for examining the robustness or significance of the r...

A recent criticism that the biological species concept (BSC) unduly neglects phylogeny is examined under a novel modification of coalescent theory that considers multiple, sex-defined genealogical pathways through sexual organismal pedigrees. A competing phylogenetic species concept (PSC) also is evaluated from this vantage. Two analytical approaches are employed to capture the composite phylog...

Recent years have seen increased interest in phylogenetic comparative analyses of multivariate data sets, but to date the varied proposed approaches have not been extensively examined. Here we review the mathematical properties required of any multivariate method, and specifically evaluate existing multivariate phylogenetic comparative methods in this context. Phylogenetic comparative methods b...

Differential coexistence among species underlies geographical patterns of biodiversity. Understanding such patterns has relied either on ecological or historical approaches applied separately. Recently, macroecology and community phylogenetics have tried to integrate both ecological and historical approaches. However, macroecology is mostly non-phylogenetic, whereas community phylogenetics is l...