Basic Amino Acid Alignment Search Model evolves a DNA sequence and compares it to the original to estimate the probability of a genetic mutation by generating a matrix called a Point Accepted Mutation (PAM) matrix.  One PAM is the amount of time it takes for 1% of the amino acids to mutate and is estimated to be about 1 million years. The PAM matrix estimates the likelihood that an amino acid in row i will replace the amino acid in column j.  Raising PAM to the nth power results in a matrix that gives us the likelihood for replacements after n time units.

The Basic Amino Acid Alignment Search Model is distributed as a ready-to-run (compiled) Java archive.   Double clicking the jar file will run the program if Java is installed.  You can modify this simulation if you have EJS installed by right-clicking within the map and selecting "Open Ejs Model" from the pop-up menu item.

Please note that this resource requires at least version 1.7 of Java (JRE).