Question: Phylogenetic tree for 16S rRNA with whole taxonomy included
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gravatar for Pawel Szczesny
4.4 years ago by
Pawel Szczesny3.2k
Poland
Pawel Szczesny3.2k wrote:

Is there available a precomputed phylogenetic tree for 16S rRNA gene that has taxonomy information included for all levels not just the leaves? In principle I'm looking for a tree that has looks like (Escherichia(Escherichia coli(Ec K12, Ec O167))) but with branch lengths. I have found a few small ones, but I'm looking for the largest possible (RDP has an alignment with 1.3M sequences, GG 300K).

 

ADD COMMENTlink modified 4.4 years ago by Joseph Hughes2.6k • written 4.4 years ago by Pawel Szczesny3.2k
2
gravatar for Joseph Hughes
4.4 years ago by
Joseph Hughes2.6k
Scotland, UK
Joseph Hughes2.6k wrote:

You can find a manually curated tree in SILVA with almost 500,000 tips: http://www.arb-silva.de/download/arb-files/

ADD COMMENTlink written 4.4 years ago by Joseph Hughes2.6k

Yes, SILVA... I should probably mention that I hope I could avoid fighting with ARB software (badly written, crashes, requires weird versions of libraries). SILVA's official exports do not contain large trees. 

ADD REPLYlink written 4.4 years ago by Pawel Szczesny3.2k

There's a development version of ARB that is supposedly a lot better than the stable old one and used by basically everyone at Max Planck. 

ADD REPLYlink written 4.4 years ago by 5heikki7.6k

Finally it worked (uff, half of the time spent looking for compatible linux version). Thanks a lot for the pointer - export went smoothly. 

ADD REPLYlink written 4.3 years ago by Pawel Szczesny3.2k
1
gravatar for 5heikki
4.4 years ago by
5heikki7.6k
Finland
5heikki7.6k wrote:

gg_13_5_otus_99_annotated_tree.gz

No comments on the quality. See the readme file for how it was made.

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by 5heikki7.6k

Thanks! It looks interesting, but the GG taxonomy collapses at genus level (see gg_13_5_taxonomy.txt). I would need to create subtrees for all species/strains and attach them to the master tree at the leaves (quite possibly I will have to do it that way). 

ADD REPLYlink written 4.4 years ago by Pawel Szczesny3.2k
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