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I want to incorporate Multiple sequence alignment into our Shiny app, i.e. allow the possibility of selecting different nucleotide sequences, and do a multiple sequence alignment in real-time. The user would define as input different nt. sequences and then a tree will pop up in the app. Do you think this is feasible?

Any recommendations and feedback are really appreciated :)

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    $\begingroup$ What do you mean by “tree”? Trees don’t really make sense for pairwise alignments. $\endgroup$ Aug 3, 2017 at 9:15
  • $\begingroup$ I agree with Konrad Rudolph, trees don't make sense with pairwise alignments. There is a pairwiseAlignment function in the Biostring package though, the writePairwiseAlignments funtion can show the alignment. $\endgroup$
    – benn
    Aug 3, 2017 at 9:21
  • $\begingroup$ I mixed up terms here, I meant multiple sequences alignment not pairwise. I have edited the question, sorry about that! $\endgroup$ Aug 3, 2017 at 9:29
  • $\begingroup$ @b.nota Pairwise alignments could be used to compute distances, and a tree could be made from the distance matrix. $\endgroup$
    – bli
    Aug 4, 2017 at 9:41
  • $\begingroup$ @bli Yes, but does it make sense? $\endgroup$
    – benn
    Aug 4, 2017 at 10:54

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The ‹msa› package on Bioconductor does exactly that.

It doesn’t hand the results on a silver platter, though: you’ll need to read the vignette carefully to learn how to use it. But after that it’s pretty powerful.

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  • $\begingroup$ "It doesn’t hand the results on a silver platter", that is very true, but some boiler plate code would go a long way since many request the same functionality from a same set of functions $\endgroup$
    – Vass
    Aug 25, 2020 at 22:05

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