The raw contigs FASTA file, the GTF annotations and the peptide sequences were downloaded from:

https://www.rosaceae.org/species/malus/malus_x_domestica/genome_GDDH13_v1.1

The hard-masked FASTA file was produced with 

~/github/plant-scripts/repeats/Red2Ensembl.py --cor 4 --msk_file GDDH13_1-1_formatted.rm.fasta GDDH13_1-1_formatted.fasta red

#Genome length: 709561391 - Repeats length: 292211379 - Repeats content: 41.182%

and then converted and sorted with the following Perl script:

perl -lne 'if(!/^>/){ s/[a-z]/N/g } print' GDDH13_1-1_formatted.rm.fasta 

The rest of files were produced by RSAT-Tools to install this genome as explained at

https://rsa-tools.github.io/managing-RSAT/genome_installation/install_organisms_FASTA_GTF.html