DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNA sequence along this tree, and displays the resulting sequences. The user can save the tree and the sequences if they want to use them in other programs. The user can control the expected rate of evolution of the sequences per unit time, and the transition/transversion ratio.
After the tree and the sequences are simulated, the program creates a randomly-chosen tree for the same species, one unrelated in structure to the true tree. The user can then rearrange the tree by hand. The resulting trees are displayed as they are made, and for each the number of base substitutions is computed that is the smallest number that would be necessary to evolve the previously simulated data on that tree. The user can then search by hand for the most parsimonious tree, and see if that recovers the true tree. The number of sites compatible with each tree is also shown, so that the user can alternatively search for the maximum-compatibility estimate of the tree.
