This program generates k random phylogenetic trees with n leaves (i.e., species, taxa) and an average branch length l using the random tree generation procedure described by Kuhner and Felsenstein (1994). The branch lengths of trees are computed using an exponential distribution. The branch lengths are multiplied by 1+ax, where the variable x is obtained from an exponential distribution (P(x>k) = exp(-k)), and the constant a is a tuning factor for the deviation intensity (as in Guindon and Gascuel (2002), the value of a is fixed to 0.8). The random trees generated by this procedure have depth of O(log (n)).

References :

Kuhner, M., and J. Felsenstein. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
Guindon, S., and O. Gascuel. 2002. Efficient biased estimation of evolutionary distances when substitution rates vary across sites. Mol. Biol. Evol. 19:534-543.

This site has been visited 711027 times since Friday, November 25, 2005.