Computational protocol: Evolution of Cariogenic Character in Streptococcus mutans: Horizontal Transmission of Glycosyl Hydrolase Family 70 Genes

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Protocol publication

[…] Sequence alignment was performed using ClustalX software version 1.83 (http://bips.u-strasbg.fr/fr/Documentation/ClustalX/#G). Multiple alignment files saved by ClustalX in the Clustal format (*.aln) were converted to the MEGA format (*.meg) using the MEGA version 5 software (http://www.megasoftware.net/). Phylogenetic analysis was performed by the NJ, ME, and MP methods using MEGA version 5 software. Phylogenetic distances were calculated by the NJ method using the same software. The corresponding parameter of the NJ algorithm was set at ‘complete deletion’, and the ‘nucleotide: p-distance’ model and ‘bootstrap method’ were used. The mean interpopulational evolutionary diversity of the sequences encoding the catalytic domain of GTFs among Streptococcus, Leukonostoc, and Lactobacillus was also calculated with MEGA 5. The ‘complete delition’, ‘bootstrap method’, and ‘p-distance’ model were used in this analysis. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Streptococcus mutans
Chemicals Sucrose, Lactic Acid