Additional section
Use branch lengths from user trees?
Yes
No

Probability model for amino acid change
Jones-Taylor-Thornton
Henikoff/Tillier PMBs
Dayhoff PAM

Rate variation among sites
Gamma distributed rates
Gamma+invariant sites
User defined HMM of rates
Constant rate

Coefficient of variation of substitution rate among sites

Number of categories (1-9)

Coefficient of variation of substitution rate among sites

Number of categories (1-9) including one for invariant sites

Fraction of invariant sites

Number of HMM rate categories

HMM category rates

Probability for each HMM category

Rates at adjacent sites correlated?
Yes
No

Mean block length of sites having the same rate

Number of times to randomise, choose 0 if you don't want to randomise

Random number seed between 1 and 32767 (must be odd)

Global rearrangements?
Yes
No

Species number to use as outgroup

Speedier but rougher analysis?
Yes
No