The tree of one percent
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* Corresponding author: Tal Dagan tal.dagan@uni-duesseldorf.de
Genome Biology 2006, 7:118 doi:10.1186/gb-2006-7-10-118
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Review
Molecular musings in microbial ecology and evolution Rebecca J Case, Yan Boucher Biology Direct 2011, 6:58 (10 November 2011) This article is part of a collection on Beyond the tree of life |
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Hypothesis
The public goods hypothesis for the evolution of life on Earth James O McInerney, Davide Pisani, Eric Bapteste, Mary J O'Connell Biology Direct 2011, 6:41 (23 August 2011) This article is part of a collection on Beyond the tree of life |
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Research
Julie Beauregard-Racine, Cédric Bicep, Klaus Schliep, Philippe Lopez, François-Joseph Lapointe, Eric Bapteste Biology Direct 2011, 6:39 (20 July 2011) This article is part of a collection on Beyond the tree of life |
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Research
Telling the whole story in a 10,000-genome world Robert G Beiko Biology Direct 2011, 6:34 (30 June 2011) This article is part of a collection on Beyond the tree of life |
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Review
How stands the Tree of Life a century and a half after The Origin? Maureen A O'Malley, Eugene V Koonin Biology Direct 2011, 6:32 (30 June 2011) This article is part of a collection on Beyond the tree of life |
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Review
Prokaryotic evolution and the tree of life are two different things Eric Bapteste, Maureen A O'Malley, Robert G Beiko, Marc Ereshefsky, J Peter Gogarten, Laura Franklin-Hall, François-Joseph Lapointe, John Dupré, Tal Dagan, Yan Boucher, William Martin Biology Direct 2009, 4:34 (29 September 2009) This article is part of a collection on Evolutionary Biology 150... From philosophical, scientific and epistemological perspectives, we argue that the tree of life can not successfully account for prokaryotic evolution, and we briefly set out alternative models to study their evolution.
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Hypothesis
On the need for widespread horizontal gene transfers under genome size constraint Hervé Isambert, Richard R Stein Biology Direct 2009, 4:28 (25 August 2009) This article is part of a collection on Evolutionary Biology 150... |
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Research article
Search for a 'Tree of Life' in the thicket of the phylogenetic forest Pere Puigbò, Yuri I Wolf, Eugene V Koonin Journal of Biology 2009, 8:59 (13 July 2009) Koonin and colleagues, comparing a forest of 7000 phylogenetic trees, discern vertical inheritance even at the earliest stages of prokaryotic evolution, despite horizontal gene transfer, but the branching order of the earliest radiations may never be resolved.
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Minireview
Kristen S Swithers, J Peter Gogarten, Gregory P Fournier Journal of Biology 2009, 8:54 (13 July 2009) Gogarten and colleagues review new research by Koonin and colleagues in Journal of Biology and explain how the obstacle of horizontal gene transfer can be circumvented to reconstruct the prokaryotic Tree of Life.
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Research article
The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods Angela McCann, James A Cotton, James O McInerney BMC Evolutionary Biology 2008, 8:312 (12 November 2008) |
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Research
Evolutionary history of bacteriophages with double-stranded DNA genomes Galina Glazko, Vladimir Makarenkov, Jing Liu, Arcady Mushegian Biology Direct 2007, 2:36 (6 December 2007) |
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Research
Kira S Makarova, Alexander V Sorokin, Pavel S Novichkov, Yuri I Wolf, Eugene V Koonin Biology Direct 2007, 2:33 (27 November 2007) |
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Research
Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo, Toni Gabaldón Genome Biology 2007, 8:R109 (13 June 2007) The human phylome, which includes evolutionary relationships of all human proteins and their homologs among thirty-nine fully sequenced eukaryotes, is reconstructed. |
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Methodology article
BranchClust: a phylogenetic algorithm for selecting gene families Maria S Poptsova, J Peter Gogarten BMC Bioinformatics 2007, 8:120 (10 April 2007) A new algorithm, BranchClust, automates the finding of gene families by phylogenetic methods, outperforming sequence-similarity methods in recognizing orthologs and paralogs in an unrestricted number of taxa, a task previously difficult to automate.
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