Hi,
I would like to play more with the phylogeny of sequences,
by selecting / removing some of the rep-seqs from the tree.
I know Qiime2 doesn't support this kind of analysis,
I work mainly on Geneious.
My question is what Mafft algorithm is used in the qiime phylogeny align-to-tree-mafft-fasttree command ?
So I can at least replicate the same alignment in another platform.
Thank you,
Maïder
Hi @Maider, welcome to the :qiime2: forum!
MAFFT, as called in q2-alignment and the various align-to-tree-mafft-* pipelines, simply uses the defaults.
If you want to know the specific set of commands called, use the --verbose option. You'll see most of the actual commands being run within the pipeline. 
For example, below is the actual command executed by mafft when running align-to-tree-mafft-fasttree
mafft --preservecase --inputorder --thread 1 /var/folders/cc/rksyds7175786_2b0vhx4rrr0000gp/T/qiime2-archive-yk8ya2xk/dfc0bcdb-d393-4d97-bf0c-ea8a0af420dc/data/dna-sequences.fasta
More information can be found in the MAFFT online manuals here and here
-Best wishes!
-Mike
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