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Foster PG, Cox CJ, Embley TM. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Philosophical Transactions of the Royal Society B: Biological Sciences. 2009;364(1527):2197 - 2207. doi:10.1098/rstb.2009.0034
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Williams TA, Foster PG, Nye TMW, Cox CJ, Embley TM. A congruent phylogenomic signal places eukaryotes within the Archaea. Proceedings of the Royal Society B: Biological Sciences. 2012;279(1749):4870 - 4879. doi:10.1098/rspb.2012.1795
Cox CJ, Li B, Foster PG, Embley TM, Civan P. Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions. Systematic Biology. 2014;63(2):272 - 279. doi:10.1093/sysbio/syt109
Li B, Lopes JS, Foster PG, Embley TM, Cox CJ. Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins. Molecular Biology and Evolution. 2014;31(7):1697 - 1709. doi:10.1093/molbev/msu105
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Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. The archaebacterial origin of eukaryotes. Proceedings of the National Academy of Sciences. 2008;105(51):20356 - 20361. doi:10.1073/pnas.0810647105
Civa  P, Foster PG, Embley MT, Seneca A, Cox CJ. Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants. Genome Biology and Evolution. 2014;6(4):897 - 911. doi:10.1093/gbe/evu061