Genome Biology

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The human phylome

Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo and Toni Gabaldón*

Genome Biology 2007, 8:R109 doi:10.1186/gb-2007-8-6-r109

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2× genomes - depth does matter

Michel C Milinkovitch, Raphaël Helaers, Eric Depiereux, Athanasia C Tzika, Toni Gabaldón Genome Biology 2010, 11:R16 (9 February 2010)

The use of low coverage genomes in comparative evolutionary analyses skews estimates of gene gains and losses.

Research article   Open Access

Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence

Marina Marcet-Houben, Giuseppe Marceddu, Toni Gabaldón BMC Evolutionary Biology 2009, 9:295 (21 December 2009)

Research   Open Access

ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets

Guan Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, Dong Xu BMC Bioinformatics 2009, 10(Suppl 1):S5 (30 January 2009)

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Large-scale assignment of orthology: back to phylogenetics?

Toni Gabaldón Genome Biology 2008, 9:235 (30 October 2008)

Automated use of phylogenetic trees to deduce orthology relationships in proteins.

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Topological variation in single-gene phylogenetic trees

Jose Castresana Genome Biology 2007, 8:216 (13 June 2007)

A large-scale phylogenetic study of the human lineage dramatically points up the problems of using single genes to build phylogenetic trees.