Question: Lowest common ancestor for taxonomy
0
gravatar for David
2.2 years ago by
David160
David160 wrote:

Hello,

I would like to know if there is any library out there to run a lowest common ancestor on the ncbi tree.

i have annotated a set of contigs into species and would like to use LCA to recover the ancestor. I have found MEGAN but it is based on java and is not very fast.

is there any tool or library out there that could be used ?' Was thinking of c++ or python implementations.

Thanks, david

tree taxonomy lca ncbi • 1.2k views
ADD COMMENTlink modified 2.2 years ago by Brian Bushnell16k • written 2.2 years ago by David160

see Last Common Ancestor From Ncbi Taxonomy Using Java

ADD REPLYlink written 2.2 years ago by Pierre Lindenbaum124k

Thanks Pierre, seems you need to submit a couple of taxids for LCA. In my case I can have many taxids to submit, not just tow taxids ??? Also forgot to mention that input file is a blasttab file.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by David160
0
gravatar for Brian Bushnell
2.2 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

With NCBI taxonomy identifiers, you can do this:

http://taxonomy.jgi-psf.org/tax/id/ancestor/9606,9612,9913

You can alternatively use the names (underscores are optional; spaces work too)

http://taxonomy.jgi-psf.org/tax/name/ancestor/homo_sapiens,canis_lupus,bos_taurus

...or just get the NCBI taxID in plaintext rather than the json-formatted lineage:

http://taxonomy.jgi-psf.org/tax/pt_name/ancestor/homo_sapiens,canis_lupus,bos_taurus

You can go to http://taxonomy.jgi-psf.org for more details. This is pretty simple to get via a curl call (just put "curl " in front of the url). Incidentally this is based on Java and very fast :)

If you want you can do this locally instead, by downloading the BBMap package, but I think the web service is the fastest.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Brian Bushnell16k

Thanks Brian, I´d rather have a local solution than relying on web queries.

ADD REPLYlink written 2.2 years ago by David160
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