The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods.

ABSTRACT:

Background

In the past decade or more, the emphasis for reconstructing species phylogenies has moved from the analysis of a single gene to the analysis of multiple genes and even completed genomes. The simplest method of scaling up is to use familiar analysis methods on a larger scale and this is the most popular approach. However, duplications and losses of genes along with horizontal gene transfer (HGT) can lead to a situation where there is only an indirect relationship between gene and genome phylogenies. In this study we examine five widely-used approaches and their variants to see if indeed they are more-or-less saying the same thing. In particular, we focus on Conditioned Reconstruction as it is a method that is designed to work well even if HGT is present.

Results

We

SUBMITTER: McCann A 

PROVIDER: S-EPMC2592249 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature