Question: Extract Tree Topology From Ncbi Taxonomy Database
1
gravatar for Lhl
6.3 years ago by
Lhl730
United States
Lhl730 wrote:

Hi There,

I am wondering if i can extract tree for a given list of species using bioperl from NCBI taxonnomy database.

I hope some of you can help me figure this out.

Many thanks in advance.

Kind Regards,

Lhl

taxonomy bioperl • 2.3k views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 6.3 years ago by Lhl730
2

Not a BioPerl solution, but this python script will do the job: https://github.com/jhcepas/ncbi_taxonomy . I wrote some more info at http://jhcepas.cgenomics.org/?p=216

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by jhc2.8k
1

something like Last Common Ancestor From Ncbi Taxonomy Using Java ?

ADD REPLYlink written 6.3 years ago by Pierre Lindenbaum117k

Not exactly, but i think it is useful.I might use it in the future. Thanks a lot.

Lhl

ADD REPLYlink written 6.3 years ago by Lhl730

Yes. This is exactly what i want.

Many thanks.

Lhl

ADD REPLYlink written 6.3 years ago by Lhl730
0
gravatar for briano
6.3 years ago by
briano0
briano0 wrote:

Lhl,

The Bioperl Bio::Tree::TreeFunctionsI module has a get_lca method. Is this what you're looking for?

Brian O.

ADD COMMENTlink written 6.3 years ago by briano0

HI Briano,

I want to get species tree given a list of species. given a list containing (speciesA, species B and Species C), i want to know how to get tree for these species. Thank you anyway. I think i might need Bio::Tree::Tree and get_lca in the future.

Cheers

Lhl

ADD REPLYlink written 6.3 years ago by Lhl730
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