Bibliography

[1] 1000 genomes project.

[2] et al Ciccarelli, Francesca. Toward automatic reconstruction of a highly resolved tree of life. Science, 311, 2006.

[3] Tal Dagan and William Martin. The tree of one percent. Genome Biology, Nov 2006.

[4] Ochman Howard Daubin Vincent, Moran Nancy A. Phylogenetics and the cohesion of bacterial genomes.

Science, 301, 2003.

[5] A.J. Enright, S. Van Dongen, and C. A. Ouzounis. An ecient algorithm for large-scale detection of

protein familes. Nucleic Acids Research, 30(7):1575–1584, Apr 2002.

[6] Stephanie Guindon and Olivier Gascuel. A simple, fast, and accurate algorithm to estimate large

phylogenies by maximum likelihood. Systems Biology, 52(5):696–704, 2003.

[7] Sanderson MJ. r8s: Inferring absolute rates of molecular evolution and divergence times in the absence

of a molecular clock. Bioinformatics, 19(2):301–302, Jan 2003.

[8] R. Thane Papke, Olga Zhaxybayeva, Edward J Fiel, Katrin Sommerfeld, Denise Muise, and W. Ford

Doolittle. Searching for species in haloarchaea. PNAS, 104(35):14092–14097, 2007.

[9] Pere Puigbo, Yuri I Wolf, and Eugene V Koonin. Search for a ’tree of life’ in the thicket of the

phylogenetic forest. Journal of Biology, 8(59), July 2009.

[10] Sagi Snir, Yuri I Wolf, and Eugene V Koonin. Universal pacemaker of genome evolution. PLoS compu-

tational biology, 8(11), 2012.

[11] Douglas L Theobald. A formal test of the theory of universal common ancestry. Nature, 465:219–222, 2010.

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