Computational protocol: Prevalence and genetic variability of Anaplasma phagocytophilum in wild rodents from the Italian alps

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Protocol publication

[…] Fisher’s exact test or Chi-squared tests were carried out to determine if there were statistical differences in the prevalence of AP between the two main rodent hosts and among sites and altitudes.Nucleotide sequences were verified using Sequencer 4.7, assembled using MEGA6 software and further aligned with ClustalW []. The alignment showed that all samples from this study were 100% identical. Therefore only one representative sequence was used for subsequent phylogenetic analysis. MEGA version 6 was used to construct a phylogenetic tree for each gene fragment (Fig. ) []. The maximum-likelihood algorithm [] with Tamura-Nei model [] were used with Felsenstein’s [] bootstrap test of 1000 iterations. The analysis involved 59 nucleotide sequences of groEl and 64 nucleotide sequences of msp4 downloaded from NCBI and 1 representative groEL and msp4 nucleotide sequence from this study (GenBank Accession nos. KX517839 and KX517840, respectively). […]

Pipeline specifications

Software tools MEGA, Clustal W
Application Phylogenetics
Organisms Homo sapiens, Anaplasma phagocytophilum, Mus musculus, Rattus norvegicus
Diseases Skin Diseases, Bacterial