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Fig. 7 | BMC Microbiology

Fig. 7

From: Carbohydrate metabolic systems present on genomic islands are lost and gained in Vibrio parahaemolyticus

Fig. 7

Phylogenetic analysis of CitF among the Vibrionaceae. This analysis involved 32 amino acid sequences representing CitF homologues present among the Vibrionaceae. Phylogeny was inferred by using the Maximum Likelihood method and Le_Gascuel_2008 model [40]. The tree with the highest log likelihood (− 7580.58) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.4398)). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. All positions with less than 95% site coverage were eliminated, i.e., fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position (partial deletion option). There were a total of 489 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [29]

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