Collaboration with Patrick's Wilson's group, led by Carole Henry: Influenza Virus Vaccination Elicits Poorly Adapted B Cell Responses in Elderly Individuals.

Sbatch script blast_B_to_reference_seqs.sbatch contains the commands used for blasting influenza B HA sequences in genbank_B_HA.fasta against the reference strains in reference_B_strains.fasta (both files are in data/sequences/). Script process_blast_output.R processes the resulting csv file into another csv file listing the assigned lineage for each isolate (identified by its name and accession number). partition_B_sequences.py takes a fasta file with sequences and the lineage assignment csv file produced by process_blast_output.R and outputs separate fasta files with sequences from the Yamagata and Victoria lineages. Shell script partition_B_sequences.sh executes partition_B_sequences.py for genbank_B_HA.fasta, genbank_B_NA.fasta and genbank_B_NP.fasta.

Commands for aligning HA, NA and NP sequences for each subtype / lineage using MAFFT are contained in the *_alignment.sbatch sbatch files.

divergence_vs_time.py uses functions implemented in alignment_analyses_functions.py to calculate % amino acid divergence and number of potential glycosylation sites over time given an alignment file, the name of a reference isolate and the range of sites to be considered. Shell scripts compute_distances*.sh execute that script for each subtype / lineage of influenza A and B.

combine_all_plots.R calls plot_divergence_vs_time.R and plot_divergence_vs_time_by_domain.R to produce the figure in the paper.