Filter representative FASTA sequences

Dear members of the community

Perform the sequencing of 4 samples with the marker RNA16s. To build the phylogenetic tree I did it following the tutorial “Moving Pictures”, however my phylogenetic tree shows many polytomies.

Based on the above I am interested in making a condensation of my phylogenetic tree, and be able to obtain fasta sequences representative of only some bacteria genera, my question is as follows Is there any kind of tutorial to be able to extract only one group of fasta sequences, to be able to generate a condensed phylogenetic tree?

I appreciate your help, best regards

Sounds like you want taxa filter-seqs. That will allow you to remove (or include) specific taxa. There is no way to “collapse” the tree to grab only representative sequences for each group, though you could use filter-seqs to select specific species that you want to use as “representatives” for each clade. Good luck!

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Thank you

However, you know if there is a way to extract the phylogeny of a particular phylogenetic group in my case the purpose is to make a phylogenetic tree per group


fragment-insertion has a filter-features method to filter fragments in a tree based on whether they are present in a feature table. So presumably you could filter you feature table to contain a particular phylogenetic group, then use that to filter those features from the phylogeny. I have not tested that approach, though, so cannot offer more specific guidance.

Good luck!