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A simple, fast, and accurate method of phylogenomic inference

Martin Wu1* and Jonathan A Eisen123

Author Affiliations

1 Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA

2 Section of Evolution and Ecology, College of Biological Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA

3 Department of Medical Microbiology and Immunology, School of Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA

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Genome Biology 2008, 9:R151  doi:10.1186/gb-2008-9-10-r151

Published: 13 October 2008

Additional files

Additional data file 1:

Presented is a table listing the 578 complete bacterial genomes downloaded from the NCBI RefSeq database for this study.

Format: DOC Size: 435KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional data file 2:

Presented is a figure of a maximum likelihood genome tree of 578 bacterial species. Major taxonomic groups are highlighted by color.

Format: EPS Size: 420KB Download file

Open Data

Additional data file 3:

Presented is a figure that compares γ-proteobacterial phylogenetic trees made from a super-matrix of 31 protein phylogenetic markers (A) and from the SSU rDNA (B). Bootstrap support values are shown along their corresponding branches.

Format: EPS Size: 171KB Download file

Open Data

Additional data file 4:

Presented is a figure of a maximum likelihood tree of rpoB. Adding a novel genome (Thermomicrobium roseum) to the reference tree helped anchor a sequence read (ZAVAM73TF) from a Yellowstone hotspring metagenomic study.

Format: EPS Size: 299KB Download file

Open Data

Additional data file 5:

Presented is a table listing phylotypes breakdown of the Sargasso Sea metagenomic sequence data by phylogenetic markers and major taxonomic groups.

Format: DOC Size: 164KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data