Fig. 3

Concatenated alignments of the 31 highly conserved COGs for the 50 members of the Pseudomonas fluorescens group described by [31], which presents a sequenced genome (draft or final) and R4 strain were made with MUSCLE [47]. The poorly aligned and divergent regions were eliminated using Gblocks [48], as described by [49]. The phylogenetic tree was reconstructed using the maximum likelihood method implemented in the PhyML v3.0 program [50] using the Dayhoff substitution model. Reliability for internal branches was assessed using the Shimodaira-Hasegawa-like Approximate-Likelihood [51]. The resulting tree was visualized using TreeGraph 2 [52]