check out PhyML (http://www.atgc-montpellier.fr/phyml/alrt/). they implement a number of different algorithms for branch support, including bootstrapping.

Hi james...I ve checked this one already...they do give the bootstraps with the trees but don't have something that can allow pruning based on bootstrap...thanks

Ah sorry about that didn't read your question carefully. One thing you could do would be to just run PhyML with bootstrap support, assign some cutoff for how much support you require, run PhyML again and use the output of the first run to specify a topological constraints file, and do this iteratively until the maximum likelihood stops improving significantly.