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 ( We used ConsensusMaker ( 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 ( 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