The script generate_fasta_4_haplotype_new.R was utilized to reconstruct haplotypes for each of the target genes in FASTA files, with sample IDs used as sequence IDs. The IDs for major and minor haplotypes were differentiated by adding "_maj" and "_min" as suffixes, respectively.
Using metadata from the samples, the FASTA sequences were separated into individual files based on their country of origin, excluding sequences with 'N'. Only major haplotypes were included in the generated files.
The R script vaxpack_in_out_args.R was developed to enable vaxpack analysis through command line arguments.
The scripts utilized in this GitHub repository were built upon the extensive work of the authors from the GitHub repository located here. Credit is duly attributed to the original authors for their contributions.