Phylogenetic tree for 16S rRNA with whole taxonomy included
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9.4 years ago

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).

taxonomy phylogenetic-tree 16S-rRNA • 5.4k views
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9.4 years ago
Joseph Hughes ★ 3.0k

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

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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.

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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.

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

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9.4 years ago
5heikki 11k

gg_13_5_otus_99_annotated_tree.gz

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

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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).

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