Bootstrap tests [Felsenstein, 1985] is one of the most common ways to evaluate the reliability of the topology of a phylogenetic tree. In a bootstrap test, trees are evaluated using Efron's resampling technique [Efron, 1982], which samples nucleotides from the original set of sequences as follows:
Given an alignment of sequences (rows) of length (columns), we randomly choose columns in the alignment with replacement and use them to create a new alignment. The new alignment has rows and columns just like the original alignment but it may contain duplicate columns and some columns in the original alignment may not be included in the new alignment. From this new alignment we reconstruct the corresponding tree and compare it to the original tree. For each subtree in the original tree we search for the same subtree in the new tree and add a score of one to the node at the root of the subtree if the subtree is present in the new tree. This procedure is repeated a number of times (usually around 100 times). The result is a counter for each interior node of the original tree, which indicate how likely it is to observe the exact same subtree when the input sequences are sampled. A bootstrap value is then computed for each interior node as the percentage of resampled trees that contained the same subtree as that rooted at the node.
Bootstrap values can be seen as a measure of how reliably we can reconstruct a tree, given the sequence data available. If all trees reconstructed from resampled sequence data have very different topologies, then most bootstrap values will be low, which is a strong indication that the topology of the original tree cannot be trusted.