Hi, I am new in Phylogenetics and therefor asking naive question. Can I use tree generated in MrBayes in RAxML to get Bootstrap support or i have to generate a new tree with same .phy file and manually compare Bootstrap values with Posterior probability values for every node.
Why would you do that? Generally speaking, bootstrapping is a method for assessing accuracy of statistical estimates. To quote directly from wikipedia:
Bootstrapping allows assigning measures of accuracy (defined in terms of bias, variance, confidence intervals, prediction error or some other such measure) to sample estimates.
The purpose of bootstrapping in phylogeny is to see how stable is your tree (constructed with a particular method), under data perturbation. For this purpose, you have to use the same method as before to reconstruct the bootstrapped trees.
I feel I am not explaining myself clearly, so the take-away message is this: original tree and bootstrapped trees have to be built under the same method, otherwise the bootstrap values are meaningless.