Computational protocol: 16S–23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads

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Protocol publication

[…] Sequences obtained were analyzed on CLC Main Workbench v5.5 and deposited to GenBank under the accession numbers indicated above. Sequences were aligned using the Clustal Omega multiple sequence alignment program () with default parameters. Phylogeny was inferred using the Maximum Likelihood method based on the Jukes–Cantor evolutionary model with the consensus tree inferred from 1,000 bootstrap replicates. The 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. All position containing gaps and missing data were eliminated, and the total data set was composed of 86 positions. Tree building along with visualization were done using the MEGA6 program () (Figure ). […]

Pipeline specifications