Computational protocol: HIV type 1 drug resistance patterns among patients failing first and second line antiretroviral therapy in Nairobi, Kenya

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Protocol publication

[…] Genotypic drug resistance in the pol-RT region was defined as the presence of one or more resistance-related mutations, as specified by the consensus mutation figures of the International AIDS Society-USA []. HIV subtyping tools, genotype (http://www.ncbi.nlm.nih.gov/projects/genotyping/formpagex.cgi), RIP (http://www.hiv.lanl.gov/content/sequence/RIP/RIP.html), and Jumping HMMER (http://jphmm.gobics.de/submission_hiv.html), were used in confirming subtyping []. […]

Pipeline specifications

Software tools HMMER, jpHMM
Application Phylogenetics
Organisms Human immunodeficiency virus 1, Human immunodeficiency virus 2, Homo sapiens