Can ETE3 list all bacterial species present in NCBI Taxonomy?

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2.2 years ago

Andrzej Zielezinski 11k

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!

NCBI ETE3 taxonomy • 668 views

ADD COMMENT • link 2.2 years ago by Andrzej Zielezinski 11k

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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.

ADD REPLY • link 2.2 years ago by GenoMax 141k

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Thanks. Yes, I would like to avoid parsing the taxonomy dump files as I have all other taxonomy-related operations already implemented using ETE3.

ADD REPLY • link 2.2 years ago by Andrzej Zielezinski 11k

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