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Fig. 2 | Standards in Genomic Sciences

Fig. 2

From: The complete genome sequence of the rumen methanogen Methanobrevibacter millerae SM9

Fig. 2

Phylogenetic tree highlighting the position of M. millerae SM9 relative to the type strains of the other species within the genus Methanobrevibacter. The evolutionary history was inferred by using the Maximum Likelihood method based on the General Time Reversible model [38]. The tree with the highest log likelihood (−4507.7026) 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 the Maximum Composite Likelihood (MCL) approach, 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 = 0.2484)]. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 15 nucleotide sequences. All positions with less than 95 % site coverage were eliminated. That is, fewer than 5 % alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 1206 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [39]. Species with strain genome sequencing projects registered in the Genomes Online Database (GOLD) [40] are labeled with an asterisk

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