Based on presentations by Dan Geiger, Shlomo Moran, and Ido ... four sequences: AAG, AAA, GGA, AGA. For example, AAA. AAA. AAA. AGA. AAA. AAG. GGA. AAA. AAA ...
The DCM phase produces a collection of trees, and the SQS phase picks the 'best' tree. ... SATe-TL vs. SATe-ML vs. Clustal. Model conditions 1-4 have long gaps ...