Computational protocol: Characterization of VP1 sequence of Coxsackievirus A16 isolates by Bayesian evolutionary method

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Protocol publication

[…] The complete VP1 sequence alignment of the CV-A16 strains was conducted with the Clustal W program in MEGA 6.0. Excess sequence was cut off, and FASTA format that can be used in the BEAST 1.8.2 was exported. Then we use the SEAL (sequence simulation and alignment evaluation software, http://tree.bio.ed.ac.uk/software/seal/) software to edit the nucleotide sequence. RDP3 Restructuring Package was used to detect the recombination of all CV-A16 sequence []. Then DAMBE was used for the saturation monitoring, if ISS < ISS.c and p = 0.0000 (extremely significant), then these sequences were unsaturated and suitable for construction of phylogenetic tree []. Finally we calculated the best alternative model With JModeltest []. The calculation was done after the selection of all the four kinds of patterns and then the statistical of AIC value. The smaller of the AIC value, the better fitting for the model with the data. Then, usually we choose the model with smallest AIC value for the construction of phylogenetic trees. [...] Bayesian Markov chain Monte Carlo (MCMC) methods were used to construct a maximum clade credibility tree (MCC) using BEASTv1.8.2 (http://beast-mcmc.googlecode.com/files/BEASTv1.8.2.tgz). Tracer v1.6 (http://beast.bio.ed.ac.uk/Tracer) was used to output analysis of sampling data, and then the Tree Annotator program was employed to output the results of MCC tree model. In the end the MCC molecular evolutionary tree graph was illustrated with FigTree1.3 (http://tree.bio.ed.ac.uk/). At the same time, Bayesian skyline plot analyses was used to reconstruct the population history of CV-A16 by measuring the dynamics of VP1 gene genetic diversity over time with 160 typical CV-A16 VP1 (Additional file : Figure S1).JModeltest result revealed that HKY was the best substitution model, and the molecular clock model chosen the Relaxed Clock: Uncorrelated Log-normal. Using the Bayesian Markov Chain Monte Carlo framework, 80 million steps were run, sampling every 8000 and removing 10 % as burn-in. Convergence was assessed using Tracer (v1.6), and effective sample size (ESS) values above 200 were accepted. […]

Pipeline specifications

Software tools Clustal W, BEAST, DAMBE, jModelTest, FigTree
Application Phylogenetics
Organisms Great Island virus