[modeller_usage] How Alignment Score is calculated.

Dear MODELLERS, When pairwise alignment score calculated by MODELLER is not parallel to the Model Accuracy. Then what is the benefit Alignment Score holds for? Benn, will you please tell me the formula for calculating Alignment Score for a pairwise alignment. What is the matrix it uses for alignment and score computation. How it is calculated.

Thanks Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA