Computational protocol: Polymorphisms of HIV-2 integrase and selection of resistance to raltegravir

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Protocol publication

[…] The HIV-2 group was determined for the 3 genes PR, RT and IN through clustering analyses using RAxML v. 7.0.4 and the GTRGAMMA model, rapid bootstrapping (100 runs), and maximum likelihood selection of the optimal tree according to the Rega and Star algorithms.Phylogenetic analyses of the IN sequences were performed as follows: the appropriate substitution model for the phylogenetic tree was selected with TOPALi v. 2.5. The Akaike information criterion (AIC) and the bayesian information criterion (BIC) chose the GTR model with invariant sites and rate variation among sites. The tree was calculated using RAxML v. 7.0.4 with 100 bootstrap replicates and is included as additional file : 'Phylogenetic analysis of the HIV-2 group A and group B IN sequences'. […]

Pipeline specifications

Software tools RAxML, TOPALi
Application Phylogenetics
Organisms Human immunodeficiency virus 2, Homo sapiens
Diseases HIV Infections
Chemicals Dichlorodiphenyl Dichloroethylene