If you want to avoid having to make this choice every time, you can change some of the constants at the beginning of the program to have it initialize itself in the proper way. At the beginning of the program are three constants that determine which kind of screen graphics the program will use. They are ibmpc0, vt520, and ansi0. This is less easy to look at. Each site evolves independently.
Different lineages evolve independently.
The probability of a base substitution at a given site is small over the lengths of time involved in a branch of the phylogeny. The expected amounts of change do not vary enough among sites that two changes in one site are more probable than one change in another. Change from an occupied site to a deletion is counted as one change. Reversion from a deletion to an occupied site is allowed and is also counted as one change. Below is a test data set, but we cannot show the output it generates because of the interactive nature of the program.