If you have already generated a tree, you will get more options in this menu:

 

Choose from this menu:

(1)  New rootless Uniform tree

(2)  New rootless Yule-Harding tree

(3)  New rooted Uniform tree

(4)  New rooted Yule-Harding tree

(5)  Change rootedness

(6)  Show the edges (it can be more than one screen)

(7)  Save in binary file

default output file: tree.bin

(8)  Save in ascii file

default output file: tree.txt

(9)  Load a tree (from binary file)

default input file: tree.bin

(10) Load a tree (from ascii file)

default input file: tree.txt

(11) Permute the leaves randomly with uniform distribution

(12) Generate random sequences on leaves

default input file: matrix.txt

default output file: seq.txt

(13) Back to the main menu

Answer:

 
The first four choices generate random binary trees with different methods. The program will ask for one more parameter: the number of leaves. Item 5 can be chosen to generate a root for a rootless tree, or erase the root of a rooted tree. Item 6 will write the edges in a special format to the screen, while 7,8 will save the tree in a file. With item 9, 10 already existing (and saved), trees can be loaded. Item 11 will just permute the labels of the leaves. The permutation is random. A very important item is the 12th. Here random sequences can be generated on the leaves of the tree. Item 13 will take you back to the main menu. Click on the menu points for more details.