Computational protocol: Evolution of Salmonella enterica Virulence via Point Mutations in the Fimbrial Adhesin

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Protocol publication

[…] PhyML 3.0 was used to generate the maximum-likelihood based DNA phylograms of fimH and concatenated MLST loci, and to derive the bootstrap proportion values from 1000 replicates under GTR substitution model. The nucleotide sequences were aligned using ClustalW with default settings . Zonal Phylogeny (ZP) analysis and associated statistics were performed using Zonal Phylogeny Software (ZPS) . The maximum likelihood (ML) phylograms as implemented in ZPS were generated by PAUP* 4.0b using the general time reversible (GTP) substitution model with codon-position specific estimated base frequencies . Sequence diversity was measured by the average pairwise diversity index (π) and the rates of nonsynonymous (dN) and synonymous (dS) mutations using MEGA version 4 . Analysis of statistical significance was performed using the z-test for π and dN/dS values . The presence of structural hotspot mutations was determined using ZPS. […]

Pipeline specifications

Software tools PhyML, Clustal W, PAUP*, MEGA
Application Phylogenetics
Organisms Salmonella enterica, Salmonella enterica subsp. enterica serovar Typhi, Salmonella enterica subsp. enterica serovar Paratyphi A
Diseases Gastroenteritis, Infection, Salmonella Infections, Mastocytosis, Systemic
Chemicals Mannose