Assessing the impact of phylogenetic reconstruction error on genetic reassortment inference in segmented viruses

This is the data that support the analysis conducted in the study Assessing the impact of phylogenetic reconstruction error on genetic reassortment inference in segmented viruses. The study we assesses the scope of signals of apparent reassortment that can arise from phylogenetic reconstruction error when comparing phylogenies from various genome segments of influenza A viruses of the H5Nx. The original viral genome sequences were downloaded from NCBI Genbank and GISAID. The objective of this study was to evaluate the contribution of phylogenetic reconstruction error to the inference of reassortment events from influenza A virus (IAV) genomes from avian hosts. The dataset deposited here consists in the files to obteain the figures nthe manuscript, including entanglement results files, subtree-prune-and-regraft (SPR) counts and sibling distances corresponding to inferred SPR events. Where applicable, data from 5 independent random subsets of 213 H5Nx genomes are included, as is the data for the maximum-diversity (control dataset). The files are organized into directories according to the corresponding analysis: Entanglement analysis data. This directory stores the numerical data that was results of quantification of the phylogenetic discordance between the hemagglutinin (HA) tree and phylogenies based on the other seven influenza virus genome segments (PB2, PB1, PA, NP, NA, MP, NS) reconstructed by applying the entanglement analysis using the library . Entanglement values are provided in the files from real data on H5Nx sequences, as well as from sequences generated under the hypothesis of no reassortment along the HA phylogeny. The simulated datasets consist of the entanglement values for five independent random samples of 213 genomes, while the maximum-diversity (control) sample is in entanglement_pruned.csv. SPR analysis data. The data in this directory is used to quantify phylogenetic discordance between the hemagglutinin (HA) tree and phylogenies derived from the other seven influenza A virus genome segments (PB2, PB1, PA, NP, NA, MP, and NS) using subtree-prune-and-regraft (SPR) distances with Espalier. The data are also from SPR counts derived from real H5Nx sequence data and from sequences simulated along the HA phylogeny without reassortment. The data sets generated by the simulation are available as a single data file (spr_counts.csv) which summarizes the number of SPR's that would be seen in the overall comparison if the simulation had been due to error in phylogenetic reconstruction rather than actual reassortation and the data sets for each segment are contained in the dist_HA_[segment]_real_sim.csv files. siblings distances for random subsets. Five directories (table_distances_subset_1 through table_distances_subset_5) contain the segment-specific data for the five random subsets of 213 genomes of influenza A virus (H5Nx) used for the analysis of the sibling distances. For each of the subsets, the HA phylogeny is compared to the PB2, PB1, PA, NP, NA, MP and NS phylogenies built using both real and simulated sequence data. These data were used to compare the sibling distances for inferred SPR events with both real and simulated data.