How to download multiple proteomes at once? I'm looking for a way to download multiple proteomes at once from one clade, as fasta. Probably from the NCBI, because it looks more user-friendly than Ensembl, but Ensembl is okay too. In the best case scenario, I would like to constrain the download to a specific clade (eg. Actinobacteria, Chloroflexi etc.), maybe with a specific RefSeq Category (eg. reference/representative genome) or even depending on the genome assembly level. Command line would probably be the best option, but if there's a direct download option it would be nice to know it as well.
Does anything like this exist? Help would be much appreciated!
You could try download-refseq-genomes. It will fetch all genomes from the NCBI FTP server that are in a specific subtree of the phylogeny. 

For example, downloading the amino acid sequences from all proteins in each genome assembly for all species belonging to Chloroflexi (NCBI taxon ID = 200795):

download-refseq-genomes.pl -t faa 200795


This will download all assemblies with status=Complete. Use option -a to download all assemblies with any status.