Computational protocol: Co-Circulation of Canine Coronavirus I and IIa/b with High Prevalence and Genetic Diversity in Heilongjiang Province, Northeast China

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Protocol publication

[…] For the phylogenetic analysis, partial sequences of the M and S genes of CCoV strains, including CCoV-I, CCoV-IIa, and CCoV-IIb strains, were retrieved from GenBank. To construct the phylogenetic trees, a multiple alignment of all target sequences was performed using ClustalX program version 1.83. Furthermore, phylogenetic trees of all target sequences were generated from the ClustalX-generated alignments by MEGA6.06 software using the neighbor-joining method []. Neighbor-joining phylogenetic trees were built with the p-distance model, 1000 bootstrap replicates, and, otherwise, the default parameters in MEGA 6. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Canis lupus familiaris, Canine minute virus, Canine parvovirus
Diseases Coinfection
Chemicals Nucleotides