Rooted tree has less taxa than masked alignment fasta file- how can I make them the same?

I want to visualize the taxa in my rep seqs file on iTOL. However, when I input either my rooted or unrooted tree into iTOL, the taxa I wanted to focus on are missing. When I look at my masked alignment fasta file, the taxa are present. When are they being lost and how can I prevent this? Note that the gene I am using to identify taxa is not 16S.

Thank you,
Stephanie

Hi @Stephanieorch,
You should be able to export your tree and open with a text reader to see if those feature IDs are missing from the tree or not. That will answer your question of where these features are being lost.

Let us know what you find!

Hi Nicholas. I figured out that I had to decrease the --p-mask-min-conservation to 0 to retain all of my sequences. Thanks!

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