The genome file is not included in this release .tar.gz. Download the genome file here: UCSC_Hcal_v1.fa.gz This release contains annotation and protein files for the Hcalv1 genome. Most likely you will use files: Hcv1av93_release/Hcv1av93_model_proteins.pep.gz The model proteins for each transcript. NB - not all transcripts had CDS. Hcv1av93_release/Hcv1av93_transcripts.fasta.gz Transcript files generated directly from the genome. May contain prematurely truncated CDS. Hcv1av93_release/Hcv1av93.gff.gz Genome annotation of transcripts. Hcv1av93_release/protein_size_table_Hcv1av93.csv A table showing the protein size differences in the within-transcript-phased transcript haplotypes, as well as which was selected for the model proteins. Hcv1av93_release/partly_phased/ Hcv1av93_release/partly_phased/h1_pilon_Hcv1av93.fasta.gz Pseudohapltype h1 of within-transcript-phased transcripts. Each transcript is derived from a single haplotype, but it is not phased with respect to all other transcripts in the genome. Hcv1av93_release/partly_phased/h1_Hcv1av93.pep.gz Putative proteins from the above fasta file. Hcv1av93_release/partly_phased/h2_pilon_Hcv1av93.fasta.gz Pseudohaplotype h2 of the within-transcript-phased transcripts Hcv1av93_release/partly_phased/h2_Hcv1av93.pep.gz Putative proteins from the above fasta file. Hcv1av93_release/phased/ Hcv1av93_release/phased/Hcv1av93_h1_phased_nucl.fasta.gz Transcripts that are from h1. Matches the whole-genome phased vcf file. Hcv1av93_release/phased/Hcv1av93_h1_phased_protein.pep.gz Proteins from the above file. Hcv1av93_release/phased/Hcv1av93_h2_phased_nucl.fasta.gz Transcripts that are from h2. Matches the whole-genome phased vcf file. Hcv1av93_release/phased/Hcv1av93_h2_phased_protein.pep.gz Proteins from the above file. Hcv1av93_release/phased/transcripts_unique_to_h1.Hcv1av93.list Transcripts that were able to be assigned to haplotype 1 (h1) of the whole-genome phasing. You probably won't need this file. Hcv1av93_release/phased/transcripts_unique_to_h2.Hcv1av93.list Same as above, but to h2. You probably won't need this file. Hcv1av93_release/phased/transcripts_shared_by_both_should_be_empty.Hcv1av93.list Intermediate check that no transcripts are shared by both haplotypes. Should be empty. Hcv1av93_release/phased/second_list_of_transcripts_shared_by_both_should_be_empty.Hcv1av93.list Final check that no transcripts are shared by both haplotypes. Should be empty.