Feel really dumb asking this, but: Please can any molecular people recommend programs or online tools for making multiple sequence alignments look pretty? I have a number of alignments (DNA and protein, some compare 2 sequences, some several) and I would like to add colours/shading to highlight similarities and differences. I can find a number or programs that will make each amino acid or nucleotide a particular colour, but that isn't what I'm after. Ideally, I would like a program that colours all the homologous regions green, all the rest red. Please can anyone help? It is purely an aesthetic thing for my thesis. Thank you.

I'm sure you could prolly do this with sybyl or one of it's add-ons, do you have that "kicking" around at uni?

Oooh, don't know that one. Ta H, I will try to find it. You rock!

If you have a computational chemistry or bioinformatics department, they will definately have it. I'm afraid to say it's not something you can just get hold of, Tripos charge a fortune for it!

The more interesting question is: who are the non-molecular people out there?

I agree with H. If all else fails you could do it manually...can clustalx be used? You can download that for free.

Thanks brajbio. I had the alignment I wanted using Clustal, but just wanted a programme to colour the areas of homology for aesthetics. I found a free, downloadable programme online called Genedoc which did exactly what I wanted - it is great and free and useful for little luddite me. Genedoc finds the residues that are conserved and also allows for motifs such as active sites to be highlighted in a different colour. It was all for making my thesis look pretty. Thanks again.

You should try BioEdit
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
It includes the ClustalW tool to make alignment
and you can customize the color.
Quite an intuitive program. I often use it.

Hi piglet while using genedoc for long seq..upto 2500 seq.it does not display first 500 seq. it comes in blue background why so? any idea?

Try GeneDoc - any colours you like! And idiot proof (even I can use it)...