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Tool to visualize alignment comparisons / Alignment diff

I generated different MSA (multiple sequence alignments) from the same set of sequences using different aligner programs (for example MAFFT, FSA, hmmalign, etc).

Is there a convenient tool for visualizing the differences between resulting alignments?

I am expecting some kind of map between columns that are mostly similar; such tool would allow to pinpoint at glance which sequence segments are unaligned in one MSA while aligned in the other MSA.

In FSA (Fast Statistical Alignment), there is a companion program called MAD which allows this, but only for FSA outputs (using the --gui option), thus not usable to compare MSA from various sources. In BAli-phy as well I think, but I also ignore if it can be used for other sources.

alignment visualization diff
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updated by Wayne Wayne • written by BlastedBadger BlastedBadger

Without doing some realignment, this might be difficult to do if the alignments don't all end up the same length.

If they do, it would actually be quite easy to treat the alignment as a table and compare positions between a 'stack' of alignments.

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written by Joe Joe

1 answer

There is a tool called hhalign from the hh-suite that takes multiple alignments and aligns them into a master alignment. It will not highlight the differences as you wish, but it should be a good starting point to do so manually.

On a global scale, it may help to convert the alignments into HMMs, and align them also using hhalign. If there are areas of significant difference between the two alignments, and thus between their HMMs, it will show up in the alignment of HMMs consensus sequences.

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written by Mensur Dlakic Mensur Dlakic

I wonder if the output from hhalign could be passed to alnvu to highlight the differences?

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written by Wayne Wayne

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