This command is used by MrBayes to write trees to a nexus tree file. Trees are written in the Newick format. For instance,
tree ((1,2),3,4);
describes an unrooted tree with taxa 1 and 2 being more closely related to each other than to taxa 3 and 4. If branch lengths are saved to file, they are given after a colon sign immediately following the terminal taxon or the interior node they refer to. An example of an unrooted tree with branch lengths is:
tree ((1:0.064573,2:0.029042):0.041239,3:0.203988,4:0.187654);
Trees that are rooted (clock trees) are written with a basal dichotomy instead of a basal trichotomy. If the tree described above had been rooted on the branch leading to taxon 4, it would have been represented as:
tree (((1,2),3),4);