Lowest common ancestor

Question

[David]

Hello,

Is there any tool available to run a lowest common ancestor from a fasta file ??? I have found MEGAN6 but i'm looking for an independent tool if it exists ??

Thanks, david

Answer 1

[Brian Bushnell]

I don't know how you would compute lowest common ancestor from a fasta file. That requires multiple specified taxa; a fasta file could contain anything, and with no other knowledge, generally I'd assume a random fasta file would represent a single organism.

If you know the organisms, you can find the lca like this:

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

If you don't know the organisms... it doesn't typically make any sense to compute lca from a fasta file. If you have a fasta file containing many organisms, you can BLAST the sequences and find a bunch of hits. Then, compute lca from the hits. You'll probably end up with the lca being something uninformative like "life" or "bacteria" in that case, which is meaningless. What are you actually trying to do, and what kind of data are you working with?

Answer 2

[David]

OOpps, Was too fast writing my question.

I have a fasta file that i have blasted (using diamond -m8) to Non redundant proteins. I would like to parse the output and find the LCA from the output. Is there any tool outhere (such as lcamapper.sh from MEgan) ??

thanks,