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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

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    $\begingroup$ 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? $\endgroup$ – terdon Dec 22 '17 at 11:09
  • $\begingroup$ Whole genome alignments of about a dozen full bacterial chromosomes. $\endgroup$ – charlesdarwin Dec 22 '17 at 11:50
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Typically I use the Mauve viewer to visualize the alignments. Are there things you find lacking in that viewer?

There are multiple threads about converting xmfa to other formats

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  • $\begingroup$ 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? $\endgroup$ – charlesdarwin Dec 22 '17 at 1:12
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    $\begingroup$ I don't think so. Mauve is a designed to find large segments of homology and is not really for per base alignments $\endgroup$ – Bioathlete Dec 22 '17 at 1:40
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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, 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 of it first.

So I am not sure if this is a solution, but maybe the tool can be of use for your research.

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  • $\begingroup$ Can ADOMA be used for whole genome alignments, e.g. bacterial genomes? Or is just for gene-size alignments? $\endgroup$ – charlesdarwin Dec 22 '17 at 10:40
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    $\begingroup$ 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. $\endgroup$ – benn Dec 22 '17 at 10:49

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