Question: Mapping 16s rRNA to a tree (fast and best ways)
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gravatar for stanislav33
16 months ago by
stanislav330 wrote:

Hello. I have two tasks to do.

1) Map a signle 16s rRNA sequence to a phylogenetic tree. I also want to vizualize it so that the part of the tree which is close to my sequence is shown, but the rest of the tree is hidden (well, because of it's size).

2) Map a list of 16s rRNA sequences to a phylogenetic tree. The vizualization should be roughly the same, but one should expect distant leaves to be shown, so the picture shouldn't have too much unrelevant information, just the important taxa, etc.

I'm looking for two ways to do it: the fast one and the right one :)

The fast one should be some online tool (NCBI does some trees, but I don't like the output) where you just put your sequence(s), set parameters and click a button. (That's for my colleagues, who are biologists)

The right one should include manipulations with original 16s rRNA databases and client-side software. I have two DB: SILVA and GreenGenes. Any comments on those two? Any other databases you know which are better? What software would you recommend to use to map sequences to preexisting trees and vizualize it and to build my own trees? The vizualization moment is crucial.

Thank you.

tree map 16s rrna • 835 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by stanislav330
1

You can use iTOL to draw the trees once you have them but not for generation.

ADD REPLYlink modified 16 months ago • written 16 months ago by Asaf5.3k

Thanks, the site looks nice. Do they have precomputed rRNA trees there?

ADD REPLYlink written 16 months ago by stanislav330
0
gravatar for stanislav33
16 months ago by
stanislav330 wrote:

No other responses on where to get the precomputed database itself?

ADD COMMENTlink written 16 months ago by stanislav330
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