Generally Newick formatted trees should work. The semicolon at the end is optional. Multiple trees can be given in a single file, each on a separate line; no more than one tree should be listed on a single line. It is not necessary to include blank lines between different trees, but it will improve readability.
Clades should be placed in brackets, with the length of the branch joining the clade to the rest of the tree listed after the clade, separated by a colon. The species names can be anything not containining the characters (, ,, ), :, or newline. However the space character should be avoided because it makes reading the data not work. An example of a valid tree is:
(ABC100:5,((DEF_37:0.004,GHI:1):0.3,JKL32:1.003,(MNO23:0.6,(MNO32:0.12,PQR:0.33):0.7):0.56):0.4)
The branch lengths are optional. If the --parsimony option (see -parsimony) is not used, branchlengths that are not specified default to 1. See the file testtrees for more examples.