We are trying to build up a phylogenetic tree from data coming from QIIME1.9 (core 75 at L7 level). Do you think it is possible although considering that we don’t have in this file the OTU reference number? Can you please advice us about the best way to inference the tree with phylogenetic distances and if you can retrieve the FASTA files from the elements in the core 75?
Thanks in advance.
Just to make sure I understand, you are talking about data that has been collapsed at level 7 taxonomy and further refined to contain only those from compute_core_microbiome.py at 75% min threshold?
Unfortunately, I don’t think conceptually it is possible to reconstruct a good phylogenetic tree with that data. We no longer have information about what OTUs you actually observed and so there’s really no sequence information available to build a tree with.
You might be able to argue that you could infer a sequence from a taxonomy at L7, but you’re still going to be hard-pressed to justify your inferred sequence to others, as taxonomy and sequence don’t always have as good of a relationship with each other as we’d hope (this is part of the broader issue of attempting to align taxonomic labels with good phylogenetic information).
Is there any other data available that we could use?
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