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Fig. 2 | Standards in Genomic Sciences

Fig. 2

From: Complete genome sequence of and proposal of Thermofilum uzonense sp. nov. a novel hyperthermophilic crenarchaeon and emended description of the genus Thermofilum

Fig. 2

16S rRNA gene Maximal-likelihood phylogenetic tree of representatives of Thermofilaceae family. The tree was constructed using the Maximum Likelihood method based on the Tamura-Nei model [39]. The tree with the highest log likelihood (−5739.3765) is shown. The percentage of trees in which the associated taxa clustered together (bootstrap test of 1000 replications) is shown next to the nodes. Initial tree(s) for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach. A discrete Gamma distribution was used to model evolutionary rate differences among sites (4 categories (+G, parameter = 0.2411)). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 38 nucleotide sequences; all were longer than 1300 nucleotides. All positions containing gaps and missing data were eliminated. There was a total of 1.227 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [40]. Thermoproteaceae branch includes 13 sequences (Additional file 5). Cultivated strains are underlined. Thermofilum uzonense strain 1807-2T is in bold. Complete 16S rRNA gene of Desulfurococcus kamchatkensis (NC_011766.1, Desulfurococcales order) was chosen as an out-group. Bar, 2 substitutions per 100 nucleotides

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