Aloha, my apologies (again!). I was hoping that there might be a general answer that I could follow, like it runs under a specific set of scripts and should be in “x” folder. Here is the script that was run to generate the phylogeny:
qiime phylogeny align-to-tree-mafft-fasttree --i-sequences QCandFT/rep-seqs.qza --o-alignment PhyloAnalysis/aligned-rep-seqs.qza --o-masked-alignment PhyloAnalysis/masked-aligned-rep-seqs.qza --o-tree PhyloAnalysis/unrooted-tree.qza --o-rooted-tree PhyloAnalysis/rooted-tree.qza --p-n-threads 14
The tree has ~ 21,000 tips, as does the alignment that was used. I may have just found the right file, but I would love it if you could confirm that. I am using this information for questions of phylogenetic diversity and distinctness in lava caves, whether that be per sample, per cave, etc. in another program.
I may be using the wrong language regarding “feature table.” What I am looking at has the samples in the columns and has the “species/OTUs/features” in the rows. The files I have looked at include:
rarefied-table-summary/feature-table.tsv (has ~ 2,000, I think b/c its rarefied)
TaxonomyAnalysis/feature-table-taxanomy.tsv (has ~12,000 rows which are OTUs not samples in this case)
QCandFT/table-summary/feature-table.tsv = ~ 21,000 rows, so I think this might be it!
Attached are the scripts for all that we ran.
(upload://2kS8Fr3cjjlLZUWPnOANU0aTR2U.txt) (16.6 KB)
I spent most of the evening looking through files that I have generated for this project, and could not find a matching a file. So, thought I might try asking.
If you can confirm that should be the matching abundance table that would “match” the labels in the phylogenetic tree, that would be very helpful.
Happy to provide any further info!