Computational protocol: A considerable proportion of CRF01_AE strains in China originated from circulating intrasubtype recombinant forms (CIRF)

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Protocol publication

[…] jModelTest v0.1.1 was used to find the best-fitting model of nucleotide substitution for the dataset 2 []. The general time reversible (GTR) model with g-distributed (G) among-site rate heterogeneity and a proportion of invariant sites (I) (the GTR + I + G model) were chosen as the most appropriate model on the basis of the standard Akaike information criterion (AIC) and Bayesian information criterion (BIC). PhyML 3.0 was used to estimate a maximum likelihood phylogenetic tree for near full-length genome (NFLG) sequences in China using the GTR + I + G nucleotide substitution model []. Tree topologies were searched heuristically using the subtree pruning and regrafting procedure (SPR). The confidence of each node in phylogenetic trees was determined using the fast-likelihood-based method of aLRT SH-like. The final maximum likelihood tree was visualized using Mega5 []. The topology of the tree was further confirmed by another round of phylogenetic analysis using a Beast tool based on Bayesian inference (data not shown). […]

Pipeline specifications

Software tools jModelTest, PhyML, MEGA, BEAST
Application Phylogenetics
Organisms Human immunodeficiency virus 1, Human immunodeficiency virus 2, Homo sapiens
Diseases Encephalitis, Arbovirus