Michael P. Dunne: Dphil Thesis, Supplementary Material

<strong>ch2</strong> 1-orthogroups (list of orthogroup members for plants and fungi) 2-passed_hits (all accepted candidate hits as listed in Table 2.9) 3-og_categories (all accepted hits belonging to various categories as listed in Table 2.10) <strong>ch3</strong> 1-juncScores (splice junction recall scores for all annotated plant and fungal transcripts) 2-covScores (coverage scores for all annotated plant and fungal transcripts) 3-aliScore (alignment score calculator) 4-DOGs (FASTA alignments for all discrepant orthogroups) 5-subcell (subcellular localisation predictions and stats for all orthogroups) <strong>ch4</strong> 1-newGenes (GTF and FASTA files for all newly obtained genes) <strong>ch5</strong> <strong> </strong> 1-results (all changed genes, with GTFs, coverage and junction scores, and AA alignments with entropy scores)