I am wondering if anyone here might understand what is going on with exporting feature tables with their phylogenetic trees because I cannot get it to work. I tried to use the ncbi.tre file, and I think the sample tree (file > export > tree) should work as well, but I cannot get them to import into QIIME2. I posted this issue on the QIIME2 forum as well: https://forum.qiime2.org/t/importing-phylogenetic-tree-from-megan/21160/4.
Has anyone else tried to do something similar?
I wanted to update this post because I am still having issues. If you see the qiime2 support, there was no simple fix.
The issue is that when I select > all leaves or select > rank > species of a tree and export as a biom file, the IDs do not match the leaves of the ncbi.tre file provided with MEGAN. Is there something I am doing wrong in MEGAN? Is there a way to avoid any classifications that are internal nodes in the ncbi.tre file? Any advice on this issue would be appreciated.