Hello,
I'm trying to create a phylogenetic tree from my representative sequences resulting from a previously performed dada2 analysis, as follows (I'm following this tutorial).
qiime alignment mafft --i-sequences rep-seqs.qza --o-alignment aligned-rep-seqs.qza
qiime alignment mask --i-alignment aligned-rep-seqs.qza --o-masked-alignment masked-aligned-rep-seqs.qza
qiime phylogeny fasttree --i-alignment masked-aligned-rep-seqs.qza --o-tree fasttree-tree.qza
I'm trying to view the resuting tree on iTOL, as suggested in the tutorial. However, its structure is definitely too complicated, and I'd like to filter something, like all the assignments showing low abundances in the samples... (I did that with qiime feature-table filter-features in a previous step, to show only certain data in heatmaps).
I don't know how to perform this in this case, anyway, since I'm only asked rep-seqs.qza, and can't act on FeatureTable directly...
How do I perform something similar in this case?
Any suggestions about how to make a phylogenetic tree more readable in general or any alternative approach? Thanks in advance.