Entering edit mode
2.5 years ago
Hi,
I know ETE3 has a bunch of useful functions that deal with NCBI Taxonomy. But is there a way to list NCBI taxonomy identifiers of all species belonging to Bacteria (taxId = 2
)? Similarly, I would also like to see the list of taxIds of all genera of Bacteria (or eventually I can get that list by looping over species lineages, but first I need to know all the species).
Thanks!
Don't know about ETE3 but
TaxonKit
(LINK) may be useful.I assume you are not keen on parsing taxonomy dump files that NCBI makes available.
Thanks. Yes, I would like to avoid parsing the taxonomy dump files as I have all other taxonomy-related operations already implemented using ETE3.