I want to download protein fasta files for a set of bird species. I have the genome assembly accessions in a file. I feel like every time I need to bulk download fasta files I've forgotten how I did it last time and the databases have all changed their websites/interfaces. I used the NCBI databases command line to download the files. However, datasets gives each accession its own folder containing "protein.faa". What I want is a single folder with fasta files so I can then use this in Orthofinder and other programmes. It's essentially useless to have a few hundred folders containing a file with the same name. Does anyone know the best way to download these files (and a way that will remain the best way and I can use it again in the future) or figure out how to use the downloads from datasets? Thank you.