This command is used to produce summary statistics for trees sampled during a Bayesian MCMC analysis. You can either summarize trees from one individual analysis, or trees coming from several independent analyses. In either case, all the sampled trees are read in and the proportion of the time any single taxon bipartition is found is counted. The proportion of the time that the bipartition is found is an approximation of the posterior probability of the bipartition. (Remember that a taxon bipartition is defined by removing a branch on the tree, dividing the tree into those taxa to the left and right of the removed branch. This set is called a taxon bipartition.) The branch length of the bipartition is also recorded, if branch lengths have been saved to file. The result is a list of the taxon bipartitions found, the frequency with which they were found, the posterior probability of the bipartition and, if the branch lengths were recorded, the mean and variance of the length of the branch.
The partition information is output to a file with the suffix ".parts". A consensus tree is also printed to a file with the suffix ".con" and printed to the screen as a cladogram, and as a phylogram if branch lengths have been saved. The consensus tree is either a 50 percent majority rule tree or a majority rule tree showing all compatible partitions. If branch lengths have been recorded during the run, the ".con" file will contain a consensus tree with branch lengths and interior nodes labelled with support values. This tree can be viewed in a program such as TreeView.
Finally, MrBayes produces a file with the ending ".trprobs" that contains a list of all the trees that were found during the MCMC analysis, sorted by their probabilities. This list of trees can be used to construct a credible set of trees. For example, if you want to construct a 95 percent credible set of trees, you include all of those trees whose cumulated probability is less than or equal to 0.95. You have the option of displaying the trees to the screen using the "Showtreeprobs" option. The default is to not display the trees to the screen; the number of different trees sampled by the chain can be quite large. If you are analyzing a large set of taxa, you may actually want to skip the calculation of tree probabilities entirely by setting "Calctreeprobs" to NO.
When calculating summary statistics you probably want to skip those trees that were sampled in the initial part of the run, the so-called burn-in period. The number of skipped samples is controlled by the "burnin" setting. The default is 0 but you typically want to override this setting.
If you are summarizing the trees sampled in several independent analyses, such as those resulting from setting the "Nruns" option of the "Mcmc" command to a value larger than 1, MrBayes will also calculate convergence diagnostics for the sampled topologies and branch lengths. These values can help you determine whether it is likely that your chains have converged.
The "Sumt" command expands the "Filename" according to the current values of the "Nruns" and "Ntrees" options. For instance, if both "Nruns" and "Ntrees" are set to 1, "Sumt" will try to open a file named "<Filename>.t". If "Nruns" is set to 2 and "Ntrees" to 1, then "Sumt" will open two files, "<Filename>.run1.t" and "<Filename>.run2.t", etc. By default, the "Filename" option should be set such that "Sumt" automatically summarizes all the results from your immediately preceding "Mcmc" command. You can also use the "Sumt" command to summarize tree samples in older analyses. If you want to do that, remember to first read in a matrix so that MrBayes knows what taxon names to expect in the trees. Then set the "Nruns", "Ntrees" and "Filename" options appropriately.
Options:
Burnin -- Determines the number of samples that will be discarded from the input file before calculating summary statistics. If there are several input files, the same number of samples will be discarded from each. Note that the burnin is set separately for the 'sumt', 'sump', and 'mcmc' commands.
Nruns -- Determines how many '.t' files from independent analyses that will be summarized. If Nruns > 1 then the names of the files are derived from 'Filename' by adding '.run1.t', '.run2.t', etc. If Nruns=1 and Ntrees=1 (see below), then only '.t' is added to 'Filename'.
Ntrees -- Determines how many trees there are in the sampled model. If 'Ntrees' > 1 then the names of the files are derived from 'Filename' by adding '.tree1.t', '.tree2.t', etc. If there are both multiple trees and multiple runs, the filenames will be '<Filename>.tree1.run1.t', '<Filename>.tree1.run2.t', etc.
Filename -- The name of the file(s) to be summarized. this is the base of the file name, to which endings are added according to the current settings of the 'Nruns' and 'Ntrees' options.
Displaygeq -- The minimum probability of partitions to display.
Contype -- Type of consensus tree. 'Halfcompat' results in a 50 majority rule tree, 'Allcompat' adds all compatible groups to such a tree.
Calctreeprobs -- Determines whether tree probabilities should be calculated.
Showtreeprobs -- Determines whether tree probabilities should be displayed on screen.
Current settings:
Parameter Options Current Setting -------------------------------------------------------- Burnin <number> 0 Nruns <number> 1 Ntrees <number> 1 Filename <name> temp.t<.t> Displaygeq <number> 0.05 Contype Halfcompat/Allcompat Halfcompat Calctreeprobs Yes/No Yes Showtreeprobs Yes/No No --------------------------------------------------------