GenomeAlignments/   contains pairwise alignment chains and nets
Genomes/            contains the genome assemblies, repeat libraries and genome-wide SpliceAI predictions
TOGA2/              contains the TOGA2 annotation, orthologs, gene loss classification, pairwise nucleotide and codon alignments

Each subfolder has a separate README.txt
Information about each genome assembly (assembly source, accession, N50s, species names and taxonomy) is given in 
  assemblies_and_species.tsv


When using these data, pls cite
Yury Malovichko et al. "TOGA2 improves speed and accuracy of comparative gene annotation and orthology inference", in preparation