Search for best tree?
Yes
No
Use lengths from user trees?
No
Yes
Global
rearrangements?
No
Yes
Transition/transversion
ratio
Use empirical
freq.
?
Yes
No
or type acg(t/u)
freq.
?
Number of substitution
category
?
1
2
3
4
5
6
7
8
9
Rate for each category?
Probability for each category?
Rates at adjacent sites correlated?
No
Yes
if yes, mean block length:
Randomize input order
of sequences?
Yes
No
If yes, choose a odd random seed
and a number of times to jumble
Number of data sets
?
Input sequence
type
?
Interleaved
Sequential
Use previous data set
?
No
Yes
if no, type data set below.
Formatted
Input Sequences as: an
example