I use UCSF Chimera (free). It shows the whole protein, not just the alignment.

http://www.cgl.ucsf.edu/chimera/

Here's how to color residues:

https://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html#MenuMouseSel

I have an inelegant solution.  I used MView to produce a formatted alignment. In the advanced parameters, I selected Alignment Width of 50. If you choose a larger alignment width, you will need to reduce the font size in Word.  There are a lot of options you can select to produce the desired overall alignment display.  Then, I just copied the results and pasted into Microsoft Word. This preserved the coloring and formatting.  After that it was possible to select individual residues or regions and just change the font color/background in Word.  

This was only really convenient with a very small alignment, because I can't select by column. I tried putting the results into Excel so I could separate the letters in the alignment into individual columns, but then I lost the color. 

If anyone has a better way of doing this, please, let us know!

http://www.ebi.ac.uk/Tools/msa/mview/

Two programs which I regularly use for this are:

Jalview (http://www.jalview.org/)

ClustalX (http://www.clustal.org/clustal2/#Download)

@Harlan R Barker

I use ClustalX 2.1 to align the sequences, but I don't see how I can select and color only the residues I want. In the "color" options I only find fixed color schemes for the entire alignment, while I would like to have most of it black, just a few residues colored or highlighted. Thanks!

try Ugene i think it will be useful for you!

Ah, I see you want to color them individually.  I don't think that ClustalX will do that, but Jalview will.  

Just select the residue(s) that you want

right click the selection to get a menu

choose 'selection'

'edit new group'

'group color'

then you can choose from a bunch of pre-defined options or choose 'user defined'

Jalview will let you export to .svg and .eps as well, which is good for publication quality images.

Thank you!

You are welcome!

I think you can also try showalign to color selected residues and save as HTML:

http://emboss.bioinformatics.nl/cgi-bin/emboss/showalign

You need to provide multiple sequence alignment results as input (for instance clustalX output),

@Nima: Eventually I need the alignment as an image, how can I do this when I have html as output?

@Harlan:  same question, how to make a nice image (with the alignment broken down to several lines so it fits on an A4 page) out of .svg or .eps?

@Britt: You can print (save as) pdf the final file. Then pdf can be loaded/imported in any graphic tool (Inkscape/photoshop...). Maybe someone has better solution for this part.

Jalview is good for coloring and editing alignments.

You can import the aligned sequences in Genedoc and choose the regions you want to highlight

I have used Genedoc for visualization of an alignment I did by using ClustalX. But in GeneDoc program there is no option to save as Pdf or something similar to that. Which program did you use at the end for making the alignment result as a figure?

@Arman: very inelegantly, I use the print screen key to create a picture of the genedoc file (often more than one picture is necessary and so I cut and paste several pictures).

This is how I did it in the end: using Jalview

1) Make the aligment in CLC and export it in format clustal

2) Open jalview and import the clustal file

3) Save it as a project

4) Select the residues to be highlighted and right mouse click “create sequence feature “. Choose the color and highlight anything else that needs to have that color immediately after. OR save the colour als a feature name, but be aware that if you change a certain feature color, all features made under that name will change color

5) Via View – wrap: make the alignment occupy several lines

6) Save!

7) Close

8) Reopen and go to file -> Export as png

9) Copy the file in the folder and change the extension to jpg

10) Right mouse click -> bewerken -> paint opens

11) Use “Select” tool + crop/cut/move

12) Save as andere indeling tiff in de juiste folder en de juiste naam

At the jalview level the alignment cannot be changed, but the names of the sequences can!

Britt Merlaen I have been looking how to do this on Jalview for the longest time! Thank you so much!

Thank you so much Britt Merlaen !!

I think Jalview will be helpful. Jalview is a free program for multiple sequence alignment editing, visualization, coloring, and analysis...

I recently used Jalview and found it useful

I've come up with another hack. I used DNAMAN software (you can use any other) for multiple sequence alignment, got output file as pdf or screenshot. Then opened the output file in MS365 PowerPoint (paid version), it has a "draw" tab in the top ribbon, here you can highlight residues specifically in different colors without any limitation. Just using your mouse; you can highlight, add different shapes or lines and finally for output file "save as" in TIF or Pdf format. Jalview is good but it also has some limitations regarding highlighting the sequence, it couldn't serve my purpose. Example image is attached here. Britt Merlaen