Computational protocol: Detection and Genetic Characterization of Relapsing Fever Spirochete Borrelia miyamotoi in Estonian Ticks

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Protocol publication

[…] Analysis and alignment of sequences was performed using BioEdit 7.0.0 software. The Maximum Likelihood model was used for phylogenetic tree reconstruction of the partial 16S rRNA (1106 bp), p66 (349 bp and 355 bp for “I. persulcatus”-type and “I. ricinus”-type, respectively) and glpQ genes (379 bp), using the Tree Puzzle program. 10 000 puzzling steps were applied using the GTP model of substitution for the partial 16S rRNA gene and the Hasegawa-Kishino-Yano (HKY) model for the partial p66 and glpQ genes. […]

Pipeline specifications

Software tools BioEdit, TREE-PUZZLE
Application Phylogenetics
Organisms Ixodes ricinus, Ixodes persulcatus, Borrelia miyamotoi, Borreliella burgdorferi
Diseases Encephalitis, Tick-Borne, Coinfection