Computational protocol: Heterosexual Transmission of Subtype C HIV 1 Selects Consensus Like Variants without Increased Replicative Capacity or Interferon α Resistance

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Protocol publication

[…] All 9kb viral sequences were aligned in Geneious bioinformatics software (Biomatters, Aukland, NZ) using MUSCLE [], followed by hand aligning. The Los Alamos National Database HIV Consensus/Ancestral Sequence Alignments were used as reference sequences (http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html). Phylogenetic trees were generated using the DIVEIN web server (http://indra.mullins.microbiol.washington.edu/DIVEIN/) []. Phylogenetic analyses were performed by maximum likelihood parsimony under Phylogeny/Divergence/Diversity. For nucleotide sequence analysis a general time reversible model was used, with a fixed gamma distribution parameter of 1, and performed with 100 bootstraps. Amino acid phylogenetic analysis was performed using the HIVw model of evolution, with 100 bootstraps []. Pairwise distances from each branch node to the subtype C consensus node were extracted from the distance matrices of the phylogenetic trees. […]

Pipeline specifications

Software tools Geneious, MUSCLE
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Human immunodeficiency virus 1, Viruses
Diseases HIV Infections