Computational protocol: Cellular immune selection with hepatitis C virus persistence in humans

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Protocol publication

[…] Genotype was determined by performing phylogenetic analysis on Core-E1 region sequences of HCV that was obtained from the first viremic specimen. For most specimens, sequences were obtained from cDNA clones that were generated with a long amplicon RT-PCR method that was described previously (). For other specimens, genotype was determined by direct sequencing of RT-PCR products from the same Core-E1 region as described previously (). Sequences were aligned using ClustalX (), and trimmed to equal length using BioEdit (). The GTR+I+G analytical model (parameters available on request from the authors) was selected using the Akaike information criterion as implemented in ModelTest version 3.06 () and PAUP* version 4b10 (Sinauer Associates). Phylogenetic trees were estimated using the neighbor-joining algorithm implemented in PAUP*, and robustness of clustering was tested by using bootstrap analysis (). […]

Pipeline specifications

Software tools Clustal W, BioEdit, ModelTest-NG, PAUP*
Application Phylogenetics
Organisms Homo sapiens
Diseases Hepatitis C, Viremia