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Table 3 True negative ortholog test set and ortholog predictions of GreenPhyl (GP), Inparanoid (INP) and BBMH (BH).

From: Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants

Arabidopsis thaliana Oryza sativa Literature UP prediction
TAIR id Alias TIGR id Alias UP PMID GP BBMH INP
- - Os03g11614.1 LHS1 0/3 16099195; 10852934 0/3 0 0
- - Os06g06750.1 MADS5      
- - Os03g54170.1 MADS34      
At5g10140.1 FLC - - 6/0 12667866;12724541; 15695584 6/0 0 0
At5g65060.2 MAF3 - -      
At5g65070.1 MAF4 - -      
At5g65050.1 MAF2 - -      
At1g77080.3 MAF1 - -      
At5g65080.1 MAF5 - -      
At3g18990.1 VRN1 - - 2/0 12667866;16549797 2/0 1/1 1/2
At1g49480.1 RTV1 - -      
At4g16845.1 VRN2 - - 1/0 12667866 1/0 0 0
  1. UP = Ultraparalogs identified in the literature; PMID = Pubmed id; GP = GreenPhyl; INP = Inparanoid