swine-influenza_vaccinated-chain.rds gives an R list made of the following items: readme contains the present description; host.table is a dataframe containing metadata about pigs in the transmission chain: ID (pig identifier), time (day of data collection), N0 (sequencing depth), M (length of sequence fragments); set.of.sequences is a list with 1 item per pig x time, each item is a list with three items: gen is a matrix providing the haplotypes that have been collected from the pig at the sampling time (1->A, 2->C, 3->G, 4->T, 5->other), IDseq gives sequence identifiers, weight is a vector providing the number of repetitions of each haplotype.