Imperial eagle scaffolds greater than 10 kb were annotated using the MAKER 2.31.9 pipeline. Briefly, we used Repeat-Masker 4.0.7 to identify and mask stretches of repetitive DNA, BLAST 2.3.0 to align avian ESTs and proteins to the genome, SNAP 0.15.4 to generate ab initio gene predictions while InterProScan 5.25-64.0 was used to identify putative protein domains. This file describes the transcript sequences associated with the annotations
