Classify Type Of Amino Acid Transitions (Acidic/Basic) Based On Their Mutations At Nucleotide Level
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.
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Is this relative to a reference sequence? Otherwise how do you define the direction acidic to basic versus basic to acidic?