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Fig. 5 | BMC Microbiology

Fig. 5

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

Fig. 5

Phylogenetic analysis of EDA1, EDA2, EDA3 and EDA4. This analysis involved 108 amino acid sequences representing EDA1, EDA2, EDA3 and EDA4 homologues present in the Vibrionaceae. The evolutionary history was inferred using the Neighbor-Joining method [26]. The optimal tree with the sum of branch length = 6.21447650 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [27]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Dayhoff matrix based method [28] and are in the units of the number of amino acid substitutions per site. The rate variation among sites was modeled with a gamma distribution (shape parameter = 5). All ambiguous positions were removed for each sequence pair (pairwise deletion option). There were a total of 213 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [29]

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