Parameters displayed on the screen and output of each program

Each program in the package will output information on the screen, and one or more files to store the results permanently. The outputs will be reviewed individually for each program in section .

The content displayed on the screen is usually quite easy to understand, but you might be a bit confused by the parameters of substitution models. PHASE outputs on the screen two kind of matrices:

one ``rate ratios'' matrix $R$

one transition matrix $Q$

These matrices are described in the transition matrices section. Other parameters have a straightforward meaning.