Phylogenetic tree for 16S rRNA with whole taxonomy included

Question

[Pawel Szczesny]

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).

Answer 1

[Joseph Hughes]

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

[Pawel Szczesny]

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.

[5heikki]

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.

[Pawel Szczesny]

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

Answer 2

[5heikki]

gg_13_5_otus_99_annotated_tree.gz

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

[Pawel Szczesny]

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).