These subfolders contain version 1 of the TOGA2 integration for different clades (mammals, birds etc). 
TOGA2 integration refers to combining and filtering multiple TOGA2 runs with different references for a single query. 
This reduces reference bias and produces a single, more complete annotation for the query species.

Version 1 refers to integrating the following TOGA2 runs:
- for mammals using human, mouse, cow and elephant as references,
- for birds using chicken, crow, kittiwake, zebra finch and emu as references, 
- for turtles using European pond turtle and Murray River turtle as references.

The per-query species folders contain
- gene annotation in bed/gtf format
- inferred query genes (bed and tsv format)
- genome browser bigBed files with UCSC decorators for visualization
- coding and protein sequences (fasta, gzipped)

For a detailed description of all output files, pls refer to the TOGA2 wiki:
https://github.com/hillerlab/TOGA2/wiki

====== REFERENCE =======
If you use the TOGA2 data, please cite:            
Yury Malovichko et al. "Accurate, comprehensive gene annotation and ortholog identification across thousands of vertebrate genomes with TOGA2", in preparation