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. 2014 Jan 24;9(1):e85131. doi: 10.1371/journal.pone.0085131

Figure 6. ML phylogenetic analysis of agrB genes from phiCDHM1 and C. difficile strains.

Figure 6

Phylogenetic analysis was performed on the agrB genes of phiCDHM1, sequenced C. difficile strains in the NCBI genome db (Oct 2011) and agrB of S. aureus subsp. aureus MRSA252. The translated sequences were aligned with MUSCLE and ML analysis performed using parameters set for the JTT nucleotide substitution model, with invariant rates, using all sites and CNI for Tree Inference and bootstrapped with 500 replicates in MEGAv5.01. Symbols correspond to those shown in Figure 4 and indicate the type of agr locus in which the gene is present (either agr1, agr2 or agr3). Taxa are abbreviated to strain names and number indicates locus type.