Answers.Body: <p>Typically I use the <a href="http://darlinglab.org/mauve/user-guide/viewer.html" rel="nofollow noreferrer">Mauve viewer</a> to visualize the alignments.  Are there things you find lacking in that viewer?</p>
  
  <p>There are multiple <a href="https://www.biostars.org/p/119721/" rel="nofollow noreferrer">threads</a> about converting xmfa to other formats</p>
  
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Answers.Text: I would like to see the sequences more zoomed in, at the base level. Do you know if it's possible with the Mauve viewer?
Answers.UserDisplayName: Biomagician
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Answers.Text: I don't think so.  Mauve is a designed to find large segments of homology and is not really for per base alignments
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Answers.Body: <p>I supervised a student a while ago, and she made a tool to focus on (i.e., visualize) SNPs in multiple alignments. The tool is called <a href="https://sourceforge.net/projects/adoma/" rel="nofollow noreferrer">ADOMA</a>, and is quite simple. It uses clustal for alignment, so I am not sure it if it may work for your Mauve data. If your data are xmfa, you'll probably have to make <a href="https://sourceforge.net/p/mauve/mailman/message/35156599/" rel="nofollow noreferrer">fasta</a> of it first.</p>
  
  <p>So I am not sure if this is a solution, but maybe the tool can be of use for your research.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-12-22T10:40:35.440Z
Answers.Text: Can ADOMA be used for whole genome alignments, e.g. bacterial genomes? Or is just for gene-size alignments?
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Answers.Text: Sorry I am not sure. The tool was made by a very good (independent working) student. It uses clustal, and if I recall correctly, clustal can also take aligned data already. So I guess your aligned data can maybe be formatted to the right input for clustal? And then adoma could in theory show only SNPs in the alignment. I think whole genome data would make very large output files, so I am not sure if it would be feasible.
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Body: <p>What software/tool can I use to visualise a multiple sequence alignment in the xmfa format as produced by command-line tool Mauve?</p>
  
  <p>I am particularly interested in seeing the single nucleotide polymorphisms on the screen.</p>
  
  <p>I am doing a multiple sequence alignment of about a dozen whole genomes, all in a single contig. </p>
  
  <p>Link to <a href="http://darlinglab.org/mauve/user-guide/introduction.html" rel="nofollow noreferrer">Mauve</a></p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-22T11:09:53.117Z
Comments.Text: What sort of alignment? How may sequences? Are you thinking reads against genome, or is this multiple full length genomic sequences aligned against each other? Since you mention mauve, should we assume whole genome alignments?
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2017-12-22T11:50:29.850Z
Comments.Text: Whole genome alignments of about a dozen full bacterial chromosomes.
Comments.UserDisplayName: Biomagician
Tags: <phylogenetics><software-recommendation>
Title: What software/tool can I use to visualise a multiple sequence alignment in the xmfa format as produced by command-line tool Mauve?
ThreadText: # What software/tool can I use to visualise a multiple sequence alignment in the xmfa format as produced by command-line tool Mauve?
  
  (Asked by: username_0 on 2017-12-21)
  
  What software/tool can I use to visualise a multiple sequence alignment in the xmfa format as produced by command-line tool Mauve?
  
  I am particularly interested in seeing the single nucleotide polymorphisms on the screen.
  
  I am doing a multiple sequence alignment of about a dozen whole genomes, all in a single contig.
  
  Link to [Mauve](http://darlinglab.org/mauve/user-guide/introduction.html)
  
  **Tags:** phylogenetics, software-recommendation
  
  > **Comments:**
  > **username_1**: What sort of alignment? How may sequences? Are you thinking reads against genome, or is this multiple full length genomic sequences aligned against each other? Since you mention mauve, should we assume whole genome alignments?  
  > **username_0**: Whole genome alignments of about a dozen full bacterial chromosomes.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2017-12-22. Score: 2 | Accepted answer
  
  Typically I use the [Mauve viewer](http://darlinglab.org/mauve/user-guide/viewer.html) to visualize the alignments. Are there things you find lacking in that viewer?
  
  There are multiple [threads](https://www.biostars.org/p/119721/) about converting xmfa to other formats
  
  > **Comments:**
  > **username_0**: I would like to see the sequences more zoomed in, at the base level. Do you know if it's possible with the Mauve viewer?  
  > **username_2**: I don't think so.  Mauve is a designed to find large segments of homology and is not really for per base alignments  
  
  ---
  
  ### Answer by username_3 on 2017-12-22. Score: 1
  
  I supervised a student a while ago, and she made a tool to focus on (i.e., visualize) SNPs in multiple alignments. The tool is called [ADOMA](https://sourceforge.net/projects/adoma/), and is quite simple. It uses clustal for alignment, so I am not sure it if it may work for your Mauve data. If your data are xmfa, you'll probably have to make [fasta](https://sourceforge.net/p/mauve/mailman/message/35156599/) of it first.
  
  So I am not sure if this is a solution, but maybe the tool can be of use for your research.
  
  > **Comments:**
  > **username_0**: Can ADOMA be used for whole genome alignments, e.g. bacterial genomes? Or is just for gene-size alignments?  
  > **username_3**: Sorry I am not sure. The tool was made by a very good (independent working) student. It uses clustal, and if I recall correctly, clustal can also take aligned data already. So I guess your aligned data can maybe be formatted to the right input for clustal? And then adoma could in theory show only SNPs in the alignment. I think whole genome data would make very large output files, so I am not sure if it would be feasible.  
  
  ---
  
  