Resampling is a statistical technique where a procedure (such as phylogenetic tree building) is repeated on a series of data sets generated by sampling from one original data set. The results of analyzing the sampled data sets are then combined to generate summary information about the original data set.
In the context of tree building, resampling involves generating a series of sequence alignments by sampling columns from the original sequence alignment. Each of these alignments (known as pseudoreplicates) is then used to build an individual phylogenetic tree. A consensus tree can then be constructed by combining information from the set of generated trees or the topologies that occur can be sorted by their frequency (see below).
Bootstrapping is the statistical method of resampling with replacement. To apply bootstrapping in the context of tree building, each pseudo-replicate is constructed by randomly sampling columns of the original alignment with replacement until an alignment of the same size is obtained (see Felsenstein 1985).
Jackknifing is a statistical method of numerical resampling based on deleting a portion of the original observations for each pseudo-replicate. A 50% jackknife randomly deletes half of the columns from the alignment to create each pseudo-replicate.