Hello everyone!
I’d like to preemptively apologize since I am completely new to microbiome (and metagenomic) analysis.
I would like to do some genus-level diversity analyses on samples curated in the microbiomeHD database (https://zenodo.org/record/569601#.X-uoRdaxVQw), which is a database of raw sequencing data taken from several studies that were then all processed through the same pipeline To this end, I need to acquire a phylogenetic tree of the OTUs in the OTU tables of the database, and it doesn’t seem to supply one. So the question is, given I have OTU tables with taxonomy assigned, and I have some taxonomy files, how to I generate a phylogenetic tree that I can use for diversity analyses?
The OTU tables provided for each one of the studies have RDP assigned taxonomy like so:
k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__;d__denovo206
And the taxonomy files have this format:
denovo206 Root rootrank 1.0 Bacteria domain 1.0 "Actinobacteria" phylum 1.0 Actinobacter ia class 1.0 Coriobacteridae subclass 1.0 Coriobacteriales order 1.0 "Coriobacterineae" suborder 1 .0 Coriobacteriaceae family 1.0 Collinsella genus 1.0
Any help would be greatly appreciated!
Guy
EDIT: I should add that I have what I believe are representative sequences for each otu table as well.