Here is a link to the Bacterial Tree of Life Project which is funded by the NSF Tree of Life Program.
Here is an overview of the project as posted on their website...
In this project, the power of genome sequencing will be harnessed to better understand the bacterial branches of the Tree of Life. This "phylogenomics" project, which will integrate genomic and phylogenetic studies, is one segment of the National Science Foundation's "Assembling the Tree of Life" program, announced this week.
The first complete genome sequence of a free-living organism was determined at The Institute for Genomic Research (TIGR) in 1995. In the years since then, complete genome sequences have been determined for a wide diversity of species including bacterial pathogens, extremophiles, protistan parasites, plants, animals, and fungi. While these include representatives from each of the three major branches in the tree of life (the Bacteria, Archaea and Eukarya) only a limited subset of each of these groups has been studied. In particular, despite the vast diversity of bacterial species and their importance as pathogens and the foundation of many ecosystems, many major groups have been neglected.
The goal of this project, a collaboration between TIGR and the Center of Marine Biotechnology (COMB), is to fill some of the gaps in our knowledge in the bacterial domain. Specifically, this project involves sequencing the complete genomes of representative strains of eight bacterial phyla. Each phylum represents a major branch in the "Tree of Life" and the phyla that were selected (Chrysiogenetes, Deferribacteres, Dictyoglomus, Nitrospira, Coprothermobacter, Synergistes, Thermodesulfobacteria, and Thermomicrobium) have not yet been explored using whole genome sequencing.
The data from these genome sequences will then be used
1. To improve the understanding of the complex phylogenetic
relationships among major bacterial phyla
2. To provide information and resources that will allow
scientists to examine the evolutionary relationships within
these poorly understood phyla in more depth than is now
3. To launch experimental studies on the biology and
physiology of organisms in these phyla.