Fig. 2

Cufflinks gave the overall highest similarity between homoeologues for test datasets of triplets of homoeologous genes. The programs Cufflinks, RSEM, Salmon, and Kallisto were compared, using two datasets that consisted of: (i) 4,307 triplets mined from the Ensembl Plants Triticum aestivum portal (“Ensembl”), and (ii) a subset of 239 triplets identified as core eukaryotic genes (“Core genes”)