A popular way of evaluating the reliability of an inferred phylogenetic tree is bootstrap analysis. The first step in a bootstrap analysis is to re-sample the alignment columns with replacement. I.e., in the re-sampled alignment, a given column in the original alignment may occur two or more times, while some columns may not be represented in the new alignment at all. The re-sampled alignment represents an estimate of how a different set of sequences from the same genes and the same species may have evolved on the same tree.
If a new tree reconstruction on the re-sampled alignment results in a tree similar to the original one, this increases the confidence in the original tree. If, on the other hand, the new tree looks very different, it means that the inferred tree is unreliable. By re-sampling a number of times it is possibly to put reliability weights on each internal branch of the inferred tree. If the data was bootstrapped a 100 times, a bootstrap score of 100 means that the corresponding branch occurs in all 100 trees made from re-sampled alignments. Thus, a high bootstrap score is a sign of greater reliability.
Other useful resources
The Tree of Life web-project
Joseph Felsensteins list of phylogeny software