A simple method for phylogenomic inference using the information of gene content of genomes.
Many studies have been contributed to the inferences of phylogenies. Some studies are based on a single-gene (family), and some are based on entire genome data. In this paper, we propose a total loss genome distance approach based on gene content information to inferring phylogenies. Through various simulations, we demonstrate and evaluate the proposed approach. We compare it with some other approaches built upon gene content or extended gene content. Overall, the proposed approach performs equally well as the other methods do and is more efficient than some of the methods. We apply our approach to 34 microbial complete genomes from COG. The reconstructed tree agrees with the results from other approaches and the tree supports the concept of universal trees.
Zhang
Hongmei
H
Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC 29208, USA.
Zhong
Yang
Y
Hao
Bailin
B
Gu
Xun
X
D001105:Archaea / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D003198:Computer Simulation; D016678:Genome; D016013:Likelihood Functions; D010802:Phylogeny; D016415:Sequence Alignment; D012984:Software