Computational protocol: Quantifying the Diversification of Hepatitis C Virus (HCV) during Primary Infection: Estimates of the In Vivo Mutation Rate

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Protocol publication

[…] Sequence alignments were initially made with ClustalW and then checked individually using JalView 2.6.1 (www.jalview.org). We used ConsensusMaker (www.HIV.lanl.gov) to calculate the consensus of the first set of sequences sampled by SGA, which is the putative T/F virus . The set of sequences from each SGA sample with the corresponding consensus was analyzed by PoissonFitter (www.HIV.lanl.gov) to calculate for each sequence the number of mutations away (i.e., Hamming distance) from the T/F, and to test whether sequence diversification conforms to a star-phylogeny and if the set of inter-sequence Hamming distances follow a Poisson distribution .Altogether we analyzed time courses of thousands of sequences with over 11.9 million base pairs and 1887 mutations . […]

Pipeline specifications

Software tools Clustal W, Jalview
Application Phylogenetics
Diseases Hepatitis C, Infection, Influenza, Human, HIV Infections