Question: Get phylum name from species name
0
gravatar for IsmailM
3.4 years ago by
IsmailM90
UK/London/University College London
IsmailM90 wrote:

Hi,

I have a list of 250 species name for which I want to get the phylum that each species belongs to...

I was wondering if there was a program or a way to use NCBI taxonomy browser to automate this.

Many thanks,

IsmailM

sequencing genome • 1.2k views
ADD COMMENTlink modified 3.4 years ago by Neilfws48k • written 3.4 years ago by IsmailM90
2

Obtain full taxonomic hierarchy from multiple species names

ADD REPLYlink written 3.4 years ago by piet1.6k
2
gravatar for Neilfws
3.4 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

To expand on the comment from piet, that link points to a previous post in which one answer uses Entrez Direct. Example usage for your case:

esearch -db taxonomy -query "Homo sapiens[Scientific Name]" | efetch -format xml | xtract -pattern Taxon -element ScientificName,Rank -tab "\n" | grep -P '\tphylum'

Chordata    phylum

 

ADD COMMENTlink written 3.4 years ago by Neilfws48k
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