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Table 3 The results of reassortant strains identified using HopPER that was validated by alternative methods for reassortment analysis

From: HopPER: an adaptive model for probability estimation of influenza reassortment through host prediction

DatasetsNumber of genomesOriginal MethodsIdentified number by HopPERTPV
Karasin et al.18Genetic and phylogenetic analyses with cycle sequencing and amplification by reverse transcription-PCR.160.889
Kingsford et al.16Enumerating maximal bicliques with a defined incompatibility graph to detect high-probability inconsistencies between the distributions of trees.140.875
Olsen et al.6Phylogenetic analysis by the method of maximum parsimony with bootstrap resampling for the genetic characterization of reassortant H3N2 viruses.61.000
Khiabanian et al.39Applying statistical methods such as diversity and entropy measures of each segment and its correlations to investigate reassortment partterns.330.846
de Silva et al.36Comprehensive analysis based on neighbourhood of each segment and using only nucleotide distance matrix as input to formulate the phylogeny.290.806
Niranjan et al.93Graph-incompatibility based reassortment finder that searches large collections of Markov chain Monte Carlo-sampled trees for groups of incompatible splits using a graph mining technique.800.860