Computational protocol: Transmission Patterns of HIV-Subtypes A/AE versus B: Inferring Risk-Behavior Trends and Treatment-Efficacy Limitations from Viral Genotypic Data Obtained Prior to and during Antiretroviral Therapy

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Protocol publication

[…] Phylogenetic and molecular-evolution analyses of protease and reverse-transcriptase (RT) sequences were performed using MEGA, version 5.05 and ClusalX (MegAlign, Lasergene version 5.01, DNASTAR Inc., Madison, WI, USA). Phylogenetic trees were drawn using FigTree v1.3.1 and branch reproducibility was assessed on 1000 replicates using Seqboot. Alignments were subjected to Bayesian Monte-Carlo Markov Chain analyses using BEAST to construct phylogenies and investigate ancestral relationships. Transmission clusters were defined as distinct populations with short branch lengths and a posterior probability ≥0.95 to have a recent common ancestor . […]

Pipeline specifications

Software tools MEGA, FigTree, PHYLIP, BEAST
Application Phylogenetics
Organisms Human immunodeficiency virus 2, Homo sapiens
Diseases HIV Infections