Phylogenetic tree construction for ASV-based amplicon data

General Discussion
1

Hi everyone,
I’d like to ask a question about phylogenetic trees.

I’m working with an amplicon-based dataset and I wanted to build a phylogenetic tree based on ASVs using bootstrapping. I first ran alignment mafft, then alignment mask, and finally phylogeny raxml-rapid-bootstrap with the following parameters:

--p-bootstrap-replicates 100 \
--p-substitution-model GTRCAT \
--p-n-threads 40 \
--p-raxml-version AVX2

However, the bootstrap step was taking more than a full day to run, so I stopped it because it didn’t seem like the best choice. I don’t have much experience with phylogenetic trees in QIIME2, so I’m wondering if this approach makes sense for ASV-based data, or if there are more appropriate or efficient methods you would recommend for building a phylogenetic tree in this case.

Any suggestions or advice would be very welcome. Thanks!

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Hi @fmglsara, We talk about some of the options at a high level in the gut-to-soil tutorial - jump to the section Building a tree for phylogenetic diversity calculations. I recommend taking a look at that, and then let us know if you still have questions.

Welcome to the QIIME 2 Forum!

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