This command compares the trees in two files, called "filename1" and "filename2". It will output a bivariate plot of the split frequencies as well as plots of the tree distance as a function of the generation. The plots can be used to get a quick indication of whether two runs have converged onto the same set of trees. The "Comparetree" command will also produce a ".parts" file and a ".dists" file (these file endings are added to the end of the "Outputname"). The ".parts" file contains the paired split frequencies from the two tree samples; the ".dists" file contains the tree distance values. Note that the "Sumt" command provides a different set of convergence diagnostics tools that you may also want to explore. Unlike "Comparetree", "Sumt" can compare more than two tree samples and will calculate consensus trees and split frequencies from the pooled samples.
Parameter Options Current Setting -------------------------------------------------------- Filename1 <name> temp.t Filename2 <name> temp.t Outputname <name> temp.comp Burnin <number> 0 ---------------------------------------------------------