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[…] Sequence alignment was performed by CLUSTAL W (BioEdit sequence alignment editor []). Neighbour-joining (NJ) trees were constructed under the Kimura 2-parameter model with the MEGA5 programme []. Sequences were individually analyzed by Simplot 3.5.1 [] and recombination analysis was then performed by bootscanning analysis []. […]

Pipeline specifications

Software tools Clustal W, BioEdit, MEGA, SimPlot
Organisms Human immunodeficiency virus 1, Human immunodeficiency virus 2, Homo sapiens
Diseases Multiple Chronic Conditions, Wiskott-Aldrich Syndrome, HIV Infections, Precursor Cell Lymphoblastic Leukemia-Lymphoma