Table 3 The results of reassortant strains identified using HopPER that was validated by alternative methods for reassortment analysis
Datasets | Number of genomes | Original Methods | Identified number by HopPER | TPV |
|---|---|---|---|---|
Karasin et al. | 18 | Genetic and phylogenetic analyses with cycle sequencing and amplification by reverse transcription-PCR. | 16 | 0.889 |
Kingsford et al. | 16 | Enumerating maximal bicliques with a defined incompatibility graph to detect high-probability inconsistencies between the distributions of trees. | 14 | 0.875 |
Olsen et al. | 6 | Phylogenetic analysis by the method of maximum parsimony with bootstrap resampling for the genetic characterization of reassortant H3N2 viruses. | 6 | 1.000 |
Khiabanian et al. | 39 | Applying statistical methods such as diversity and entropy measures of each segment and its correlations to investigate reassortment partterns. | 33 | 0.846 |
de Silva et al. | 36 | Comprehensive analysis based on neighbourhood of each segment and using only nucleotide distance matrix as input to formulate the phylogeny. | 29 | 0.806 |
Niranjan et al. | 93 | Graph-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. | 80 | 0.860 |