text: user4401: 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!
  
  user1802: 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.
  
original_text: 4401: <p>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!</p>
   1802: <p>You could try <a href="https://github.com/pmenzel/download-refseq-genomes" rel="nofollow noreferrer">download-refseq-genomes</a>. It will fetch all genomes from the NCBI FTP server that are in a specific subtree of the phylogeny. </p>
  
  <p>For example, downloading the amino acid sequences from all proteins in each genome assembly for all species belonging to Chloroflexi (NCBI taxon ID = <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&amp;id=200795&amp;lvl=3&amp;keep=1&amp;srchmode=1&amp;unlock" rel="nofollow noreferrer">200795</a>):</p>
  
  <pre><code>download-refseq-genomes.pl -t faa 200795
  </code></pre>
  
  <p>This will download all assemblies with status=Complete. Use option <code>-a</code> to download all assemblies with any status.</p>
  