How to add the amount of conservation (*);(:);(.) to an established multiple sequences alignment?

Question

[cornflower.9aceeb]

I would like to add the conservation data to my multiple sequences alignment (i generated it before, but it was saved in FASTA format and i don't have the conservation data; '*': Exact, ':': Conserved Substitution, '.': Semi-conserved substitution). Is there any way to do it? Thank you.

Answer 1

[Mensur Dlakic]

This is not exactly what you are asking for, but still it may be helpful.

http://prodata.swmed.edu/al2co/al2co.php

In one of its several outputs it will print a number above each alignment column, where 9 is absolutely conserved and 0 is completely random. The program can be downloaded here for local use.

[cornflower.9aceeb]

I will try it, thank you for your recommendation.

Answer 2

[cornflower.9aceeb]

For anyone who has the same question, you can use unipro UGENE to save as the multiple sequence alignment along with the conservation data (as a Clustal file format).