ABSTRACT

Phylogenies, the (reconstructed evolutionary histories of groups of organisms or other biological units, have become ubiquitous in biological and biomedical research. As high-throughput methods find their way into every area of the life sciences, largescale analyses are rapidly becoming a necessity; phylogenetic analysis is no exception. Indeed, renewed attention to the reconstruction of the Tree of Life, a phylogeny of all species on this planet, has served to stress the need for more accurate, robust, and efficient computational approaches to phylogenetic reconstruction. This chapter reviews the basics of phylogenetic reconstruction, highlights the scaling issues we are facing today, discusses the most promising solutions currently under development,

3.1 Phylogenetic Reconstruction: What and Why? .............................................30 3.1.1 Phylogenies ........................................................................................30 3.1.2 Phylogenetic Reconstruction .............................................................. 31 3.1.3 Data Used in Phylogenetic Reconstruction ........................................ 32 3.1.4 Scaling Issues ..................................................................................... 33 3.1.5 Reconstructing the Tree of Life .........................................................34