Computational protocol: Characterization of the patterns of drug-resistance mutations in newly diagnosed HIV-1 infected patients naïve to the antiretroviral drugs

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Protocol publication

[…] All 255 HIV-1, sequences (1302 nt) were aligned and compared with reference sequences for the Major HIV-1 subtypes, available at: http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html using CLUSTAL X []. The sequences were then manually edited with the Bioedit program [], and gaps were removed from the final alignment. All sequences were analyzed using the REGA HIV-1 subtyping tool. []Separate trees were then generated using F84 Model of substitution with both NJ and Maximum Likelihood (ML) tree building methods [], for both non-B pure subtypes and putative recombinant forms.Phylogenetic trees were performed with different evolutionary model according to the Hierarchical Likelihood Ratio Test (HLRT) implemented in the Model Test V3.0 software []. The statistical robustness within each phylogenetic tree was confirmed with a bootstrap analysis using 1000 replicates for the Neighbor-Joining (NJ) tree. All calculations were performed with PAUP*4.0 software [].Simplot software version 3.2 [] was used to generate similarity plots and bootscan plots, for genetic diversity and intersubtype recombination analysis. […]

Pipeline specifications

Software tools Clustal W, BioEdit, REGA HIV Subtyping Tool
Application Phylogenetics
Organisms Human immunodeficiency virus 1, Homo sapiens, Human immunodeficiency virus 2
Diseases Infection, HIV Infections