Answers.Body: <p>The <a href="https://bioconductor.org/packages/release/bioc/html/msa.html" rel="nofollow noreferrer">‹msa› package on Bioconductor</a> does exactly that.</p>
  
  <p>It doesn’t hand the results on a silver platter, though: you’ll need to <a href="https://bioconductor.org/packages/devel/bioc/vignettes/msa/inst/doc/msa.pdf" rel="nofollow noreferrer">read the vignette</a> carefully to learn how to use it. But after that it’s pretty powerful.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-25T22:05:33.843Z
Answers.Text: "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
Answers.UserDisplayName: Vass
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-03T09:31:47.057Z
Answers.LastActivityDate: 2017-08-03T09:31:47.057Z
Answers.UserDisplayName: Konrad Rudolph
Body: <p>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?</p>
  
  <p>Any recommendations and feedback are really appreciated :)</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-03T09:15:15.303Z
Comments.Text: What do you mean by “tree”? Trees don’t really make sense for pairwise alignments.
Comments.UserDisplayName: Konrad Rudolph
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-03T09:21:16.060Z
Comments.Text: 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.
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-03T09:29:16.290Z
Comments.Text: I mixed up terms here, I meant multiple sequences alignment not pairwise. I have edited the question, sorry about that!
Comments.UserDisplayName: Sergio Arredondo
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-04T09:41:45.023Z
Comments.Text: @b.nota Pairwise alignments could be used to compute distances, and a tree could be made from the distance matrix.
Comments.UserDisplayName: bli
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-04T10:54:50.190Z
Comments.Text: @bli Yes, but does it make sense?
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-04T13:22:57.937Z
Comments.Text: @b.nota I think that in theory, a multiple alignment is more apt to capture relevant homologies. So if the tree is meant to represent the phylogeny of the sequences, multiple alignment is theoretically better. That said, there might be practical reasons for which one would have to work with pairwise distances instead.
Comments.UserDisplayName: bli
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-04T13:27:45.370Z
Comments.Text: @bli, okay thanks for your thoughts. I do still agree, however, with Konrad that trees for pairwise alignments don't really make sense.
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-25T22:10:41.220Z
Comments.Text: @SergioArredondo, as the question is closed I cannot provide an answer, but a relevant newer question provides a MWE that shows an outline for the situations where the nucleotides are stored in an msf format, but that can be changed accordingly as other formats can be specified `https://bioinformatics.stackexchange.com/a/14160/9311` (and real time is tricky given some of the datasets can be large)
Comments.UserDisplayName: Vass
Tags: <r><phylogenetics>
Title: Multiple sequence alignment with R
ThreadText: # Multiple sequence alignment with R
  
  (Asked by: username_0 on 2017-08-03)
  
  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 :)
  
  **Tags:** r, phylogenetics
  
  > **Comments:**
  > **username_1**: What do you mean by “tree”? Trees don’t really make sense for pairwise alignments.  
  > **username_2**: I agree with username_1 username_1, 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.  
  > **username_0**: I mixed up terms here, I meant multiple sequences alignment not pairwise. I have edited the question, sorry about that!  
  > **username_3**: @b.nota Pairwise alignments could be used to compute distances, and a tree could be made from the distance matrix.  
  > **username_2**: @username_3 Yes, but does it make sense?  
  > **username_3**: @b.nota I think that in theory, a multiple alignment is more apt to capture relevant homologies. So if the tree is meant to represent the phylogeny of the sequences, multiple alignment is theoretically better. That said, there might be practical reasons for which one would have to work with pairwise distances instead.  
  > **username_2**: @username_3, okay thanks for your thoughts. I do still agree, however, with username_1 that trees for pairwise alignments don't really make sense.  
  > **username_4**: @username_0, as the question is closed I cannot provide an answer, but a relevant newer question provides a MWE that shows an outline for the situations where the nucleotides are stored in an msf format, but that can be changed accordingly as other formats can be specified `https://bioinformatics.stackexchange.com/a/14160/9311` (and real time is tricky given some of the datasets can be large)  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-08-03. Score: 4
  
  The [‹msa› package on Bioconductor](https://bioconductor.org/packages/release/bioc/html/msa.html) does exactly that.
  
  It doesn’t hand the results on a silver platter, though: you’ll need to [read the vignette](https://bioconductor.org/packages/devel/bioc/vignettes/msa/inst/doc/msa.pdf) carefully to learn how to use it. But after that it’s pretty powerful.
  
  > **Comments:**
  > **username_4**: "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  
  
  ---
  
  