Computational protocol: Population-associated differences between the phase variable LPS biosynthetic genes of Helicobacter pylori

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Protocol publication

[…] Sequences were assembled using the program Gap4 from the Staden package []. Multiple alignments were performed using ClustalW [], and then, manually edited using Seqlab from the Wisconsin Package, version 10.2 (Genetics Computer Group, Madison, Wisconsin) through the Oxford University Bioinformatics Centre. Analyses of nucleotide identity, genetic distances, and synonymous/nonsynonymous substitutions [] were performed on multiple alignments using Swaap 1.0.0 (Pride, D.T. (2001). Swaap 1.0.0: a tool for analysing substitutions and similarity in multiple alignments. Distributed by the author, available at ) []. Neighbour-joining trees [] based on distances with Kimura two-parameter estimates [] were constructed, and their robustness was assessed using a bootstrapping procedure (500 repetitions) [] using MEGA version 2.1 []. […]

Pipeline specifications

Software tools Staden, Clustal W, MEGA
Application Phylogenetics