I am looking for a multiple-sequence editor, in particular for protein sequences, that colors/highlights residues only by their type, not by their conservation. It should also allow to edit the sequences themselves, not just the position of gaps.
For a long time, I have been using GDE for this purpose. However, since the last linux update I can no longer get it to work, mostly because it relies on the ultra-outdated xview libraries. Since then, i have been looking for a suitable replacement.
However, it appears like all available MSA editors have the mandatory feature that they color the displayed residues by their degree of conservation or their similarity to a reference sequence. I understand why people might find this useful, but I personally find it annoying. If I introduce a gap at one point in the alignment, I find it totally confusing that this leads to color changes all over the alignment, just because the shift changes the overall conservation pattern. I would appreciated it if these feature could be switched off.
Any ideas?
Thanks for the suggestion! I had tried Jalview before, but discarded it because it (apparently) only allows to edit the alignment (moving gaps around) but not the sequences themselves. This feature is crucial for me, I use the MSA to visually identify regions where sequences are wrong and replace wrong or questionable parts by the letter X. Also Jalview is very slow and display lags behind the keystrokes (fatal if you keep the delete key pressed for deleting 100 residues)
You can give MEGA a try: https://megasoftware.net/
It is an entire evolutionary biology program but does include an alignment tool/editor.