What Algorithm does Qiime use by Default for Multiple Sequence Alignment When Using MAFFT?

Hi everyone,
I am curious about which strategy is used to perform multiple sequence alignment in Qiime 2. For example on MAFFT’s website they list multiple progressive and iterative methods that can be used to align sequences. I realize that each method has its pluses and minuses and I was hoping to gain some additional clarity on which method is used by default in Qiime. Thanks so much!

Hello Andrew,

I looked through the code for the alignment plugin, and I think I found the code:

Looks like this plugin uses the mafft defaults for version >=7.310. :man_shrugging:

Any comments? Suggestions?



@colinbrislawn Thank you! I was curious about which method was used as I work to figure out an unrelated problem.


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