Computational protocol: Independent evolution of macrophage-tropism and increased charge between HIV-1 R5 envelopes present in brain and immune tissue

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Protocol publication

[…] Complete gp160 env nucleotide sequences were assembled and aligned using Clustal × [] with manual adjustment. All positions with an alignment gap of one or more nucleotides were excluded.Phylogenetic and molecular evolutionary analyses were conducted using MEGA version 5 []. Maximum likelihood phylogenetic trees were generated using General Time Reversible Substitution Model using a discrete Gamma distribution with 5 rate categories and by assuming that a certain fraction of sites are evolutionary invariable for subjects CA110, 7766 and 6568 and without invariant sites for subjects NA20 and 10017. Bootstrap analyses on 1,000 replicates was used to assess the robustness of the tree. Significant (≥ 70%) bootstrap values were assigned to internal tree nodes. Reference sequences representing three HIV-1 group M subtype B http://www.hiv.lanl.gov/ envelopes (FR.83. HXBc2. K03455; TH.90.BK132.AY173951;US.98.1058 11.AY331295) were used as outgroups. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Human immunodeficiency virus 1, Homo sapiens
Diseases Acquired Immunodeficiency Syndrome, Central Nervous System Diseases, HIV Infections, Macrophage Activation Syndrome