Dear Sergei,

Have we settled yet on a format for different trees on a dataset i.e.

1-120
((a,b),(c,d));
121-190
((a,c),(b,d));

If so, it would be good to have a batch file to perform a Shimodaira-Hasegawa test for differences between trees for a given partition, summary statistics for the differences and similarities (maximum forest, etc.), and an output of the log-likelihood differences on a site-by-site basis, in order to identify sites that are contributing to the different phylogenetic signal.

Best,
Simon