How to keep track of alignment positions after profile alignments?

Question

[microbeatic]

Hello,

Is there a program/way that will keep track of the positions of column before and after profile alignments?

For example, muscle does profile alignment fine, but doesnt output which column from alignment 1 was aligned to which column in alignment 2.

Thanks

[d3p]

What format do you want that info in? if I understand your question correctly, you can just count the number of non gaps and that is the original position. But reporting that number in a useful way is the tough part

[microbeatic]

Its fasta format.

I have been comparing column abundance before and after the alignment, but running into troubles to resolve one to many similarities.

Removing gap should work, but my original alignment may contain all gap columns too.