Mapping 16s rRNA to a tree (fast and best ways)
1
0
Entering edit mode
4.0 years ago

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.

16S rRNA map tree • 1.8k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
4.0 years ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 1899 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6