A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection

Figure 1

Flowchart representing the bioinformatics pipeline. Shared Mutation Analysis workflow is indicated by green arrows. Covariance Analysis workflow is indicated by red arrows. Both branches of the pipeline require an aligned viral sequence file in fasta format. Immunological data are optional and can be both experimental or bioinformatics predicted.