Computational protocol: Reverse transcriptase drug resistance mutations in HIV-1 subtype C infected patients on ART in Karonga District, Malawi

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Protocol publication

[…] Sequence chromatographs were edited in SeqMan (DNASTAR, Inc) and all sites that showed ambiguities (two or more peaks of equal, or almost equal, height) were noted. Multiple alignments were assembled of all subtype C sequences generated with the 57 reverse transcriptase sequences generated from [] using MacClade 4.0 (Sinauer Assoc). Sequences were submitted for analysis of DRMs to the Stanford Database []. To check for transmission of DRMs, phylogenetic trees were reconstructed using the LANL subtype C ancestral sequence as outgroup under the GTR + gamma model of DNA substitution implemented RAxML7.0.3 [] with all parameters optimised by RAxML. Confidence levels in the groupings in the phylogeny were assessed using 1000 bootstrap replicates as part of the RAxML phylogeny reconstruction.Permission for the study was received from the National Health Sciences Research Committee, Malawi, and the Ethics Committee of the London School of Hygiene and Tropical Medicine, UK […]

Pipeline specifications

Software tools MacClade, RAxML
Application Phylogenetics
Organisms Homo sapiens
Diseases Heart Failure, Hepatitis C, Chronic
Chemicals Sodium