Computational protocol: Diverse Genotypes of Yersinia pestis Caused Plague in Madagascar in 2007

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Protocol publication

[…] Clinical samples that were successfully genotyped using MLVA were analyzed in conjunction with data from 262 previously published samples in a neighbor-joining analysis to determine MLVA subclades []. Phylogenies were then constructed using the SNP, MLVA, and CRISPR data for the successfully genotyped clinical samples, with separate phylogenies generated for Groups I and II (as determined by SNP data) for the MLVA and CRISPR based phylogenies ( and ). The MLVA based phylogenies were generated in MEGA6 [] as neighbor-joining dendrograms using mean character based distance matrices and include bootstrap values ≥50 generated in PAUP 4.0b10 (D. Swofford, Sinauer Associates, Inc., Sunderland, MA) based upon 1,000 simulations. The geographic distributions of the identified MLVA subclades were mapped using ArcGIS 10.2.1 for Desktop (ESRI, Redlands, CA) (). […]

Pipeline specifications

Software tools MEGA, PAUP*
Application Phylogenetics
Organisms Yersinia pestis, Homo sapiens
Diseases Plague