when analysing 16s metagenomic data, its easy to align all of your otu sequences and build a tree in order to e.g. calculate UniFrac distances. However, with shotgun metagenomic results I cannot find a simple way to get a tree of the taxa I am interested in. I've looked at the usual databases, Silva, NCBI, RDP etc. but none of them seem to have a facility to obtain a tree from a list of taxa. Does anyone know a way to do this? I could download all the 16s for my list of taxa and align and draw a tree from that, but hoping there is a way to do it from the list of taxa alone.
Thanks for any help,