I don’t think there is a straightforward answer to the gaps in a column issue. Sometimes, you might want it to show as conserved when there is a gap and other times, you want it to show as unconserved since a gap is allowed at that position.
In the original AMAS program that this feature is based on in Jalview (see this pdf)
and a server that implements the method – this was the first web server from my group – we keep it looking “retro” for this reason!
https://www.compbio.dundee.ac.uk/www-amas/
There is flexibility over how you treat gaps. AMAS is for hierarchical analysis of residue conservation and reflects the fact that sequences fall onto a tree.
Though AMAS is comprehensive, Jalview lets you explore conservation interactively. In Jalview you can subset the alignment by clustering on a tree and then look at conservation within each sub group. I find this the most useful when looking at alignments interactively since gapped sequences will typically group together and you can look at the conservation in the column in context with the hierarchical tree, then map across to structure or back to the genomic sequence.
One of the Jalview videos covers this kind of sub-family analysis on trees and I think is one of the more powerful features of Jalview for exploring column similarities and differences:
https://www.youtube.com/watch?v=8VRy9rO7Zrc
I hope all this helps?
All the best,
Geoff
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Geoff Barton FRSE FRSB | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee | Scotland, UK | email: