Classify Type Of Amino Acid Transitions (Acidic/Basic) Based On Their Mutations At Nucleotide Level

Question

[munch]

I want to detect if there is in a multiple sequence alignment more basic to acidic or acidic to basic amino acid transitions based on their mutations at nucleotide level. For example:

Basic: Histidine, Lysine, Arginine
Acidic: Aspartate, Glutamate, Asparagine, Glutamine

Is there any software package which can help me to solve this problem? Thank you in advance.

[Joseph Hughes]

Is this relative to a reference sequence? Otherwise how do you define the direction acidic to basic versus basic to acidic?