Which alignment algorithm should I use

I am a beginner of microbiome data preprocessing and qiime2. I have done the quality control by DADA2 and want to build a phylogenetic tree to calculate diversity. According to moving picture tutorial, I need to align sequences first. The algorithm provided is mafft while some other methods are provided in qiime like pynast, muscle or infernal. Some of them need template. Is there a recommendation on which one is the best or used popularly? Also, are there anyways to use pynast, muscle in qiime2?

Thanks in advance.


Hi @lindd, thanks for writing! Currently QIIME 2 only supports MAFFT for alignment, and I think at this time we are not planning on supporting pynast (I could be wrong though, one of the other QIIME 2 devs will update this topic if that is the case). I am not sure where muscle and infernal sit right now in terms of plugin priority — do you have any thoughts or preferences? Thanks!

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