Computational protocol: The second molecular epidemiological study of HIV infection in Mongolia between 2010 and 2016

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Protocol publication

[…] Statistical analysis was performed using IBM SPSS Statistics Version 23 (IBM Japan, Tokyo). The reference sequence for phylogenetic analyses was obtained from the Basic Local Alignment Search Tool (BLAST) of the National Center for Biotechnology Information (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and the HIV database of the Los Alamos National Laboratory (https://www.hiv.lanl.gov/content/index). The sequence data were aligned by ClustalW. Phylogenetic analysis was conducted by MEGA 7.0.26 [] using the neighbor-joining method and Kimura 2-parameter model with 1,000 bootstrap replications. A cluster was defined when the bootstrap score was ≥90%. The HIV-1 subtype and circulating recombinant form (CRF) were determined by the phylogenetic analysis described above, the Recombinant Identification Program in the HIV database of the Los Alamos National Laboratory, and SimPlot 3.5.1 []. The breakpoints of recombination were drawn using the Recombinant HIV-1 Drawing Tool v2.1.0 in the HIV database of the Los Alamos National Laboratory. For the data obtained from MiSeq, trimming and filtering of the sequence data was conducted by the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html), de novo assembly was conducted by VICUNA [] and mapping was conducted by BWA-MEM []. The time to the most recent common ancestor (tMRCA) was estimated by maximum clade credibility (MCC) tree analysis using the Bayesian Markov chain Monte Carlo (MCMC) method. The analysis was conducted by BEAST 2.4.3 [] with 100,000,000 states, logged every 10,000 states, and 10% burn-in. A general time reversible model with gamma distribution and invariant sites, relaxed clock log normal model, and coalescent exponential population model were adopted because of the favorable Bayes Factor analyzed by Tracer 1.5.0 in the BEAST package. A cluster was defined when the posterior probability was ≥0.9. Extended Bayesian skyline plot analysis was performed by BEAST, then effective population size was illustrated by RStudio 1.0.44 (https://www.rstudio.com). […]

Pipeline specifications

Software tools SPSS, BLASTN, Clustal W, MEGA, SimPlot, RecDraw, FASTX-Toolkit, VICUNA, BWA, BEAST
Applications Miscellaneous, Phylogenetics
Organisms Human immunodeficiency virus 1, Homo sapiens, Human immunodeficiency virus 2
Diseases HIV Infections