<p>Hello,</p>

<p>When using NCBI&#39;s interface I can exclude species, genus, even phyla. Is there a way to do that in command line blast?</p>

<p>I need to exclude one species from my search. I see this can somehow be done with a GI list, but the example they give is not very understandable.</p>

<p>Adrian</p>

Use NCBI's taxonomy browser and link from there to genbank GI list of all nucleotides or proteins. Download that and use it in the command line blast, for example from <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock">here</a> to <a href="http://www.ncbi.nlm.nih.gov/protein/?term=txid9606[Organism:exp]">here</a>, then "send to" -> "file" -> "GI list"