Computational protocol: Genome-wide analysis of codon usage bias in Bovine Coronavirus

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Protocol publication

[…] In order to gain insight into the genetic variability and evolution of BCoV, a phylogenetic tree analysis was performed for all BCoV strains enrolled in these studies, using complete genome codes. Sequences were aligned using the MUSCLE program []. Once aligned, the FindModel program (available at: https://www.hiv.lanl.gov/content/sequence/findmodel/findmodel.html) was used to identify the optimal evolutionary model that best fitted our sequence dataset.Akaike information criteria (AIC) and the log of the likelihood (logL) indicated that the GTR+ Γ model was the most accurate (AIC = 60,864.73, logL = −30,423.36). Using this model, maximum likelihood trees were constructed using software from the MEGA 6 program []. As a measure of the robustness of each node, we employed the bootstrap method (500 replicas). […]

Pipeline specifications

Software tools MUSCLE, MEGA
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Bovine coronavirus, Bos taurus, Viruses, Human poliovirus 1 Mahoney
Diseases Respiratory Tract Infections