Bootstrap percentages can be displayed on your tree when the Show Branch Labels option is selected, and Display is set to Consensus support (%) (this may be called Bootstrap support % if you have used one of the plugins to build your tree). You can alter whether the bootstrap value is displayed in the middle of the branch or next to the node by selecting the Show next to node box.
This option will only be available when you have specified that bootstrapping is performed. For the Geneious tree builder, you will need to ensure that Resample Tree is selected, and that the Resampling method is set to Bootstrap.
Bootstrapping in other tree builders
PHYML: Select Bootstrapping under the Branch Support option
PAUP*: Ticket the Perform Bootstrapping box.
RAXML: Choose the Algorithm Rapid bootstrapping and search for best-scoring ML tree.
This will output two files: the first, called <alignment_name> RAxML Bootstrapping Trees contains all the individual bootstrap trees. The second file is called <alignment_name> RAxML tree. This contains the Best scoring ML tree, and has the associated bootstrap support values calculated from the individual bootstrap trees. Under Show Branch Labels, the option Bootstrap support % will display these values on your tree.
MrBayes: Bootstrap values are not calculated on Bayesian trees, instead Posterior Probabilities are used as a measure of branch support. These can be displayed in the same way as bootstrap values by viewing the Tree View in the Posterior output file, and selecting Posterior Probability under Show Branch Labels.