exracting sequences with taxonomic annotation for phylogenetic tree

I am looking for a way to generate a fasta file containing sequences of only most abundant Otus (for example say only 500 most abundant Otus or less number) along with their taxonomic identification in the header like this (>taxonomy). Actually, I want to use this file for cophylogeny analysis. Does it make sense?
I tried to plot cophylogeny using the tree I generated in qiime2 but that is too complicated and big so cophylogeny plot is not clear. So i thought to reanalyze using this approach where I will focus only on most abundant otus for generating small and clear phylogenetic tree. Do you think this way makes sense?

Best Regards

Hi @sanda,

I think there are a few ways to get what you need and it will be up to you to decide on the best strategy for your data, but generally speaking, it sounds like the feature table filtering methods are what you’re after. Taking a look at the filtering data tutorial would be a great place to start. Note that if you type qiime feature-table --help you will notice an additional method, filter-features-conditionally, which is not yet covered in the tutorial.

I can’t comment on your other question about whether or not your strategy makes sense. I’m guessing others will need more details about your analysis to comment because “it depends” :tm: .

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