The simulations described in chapter 3 exemplify the problems that may arise when one reconstructs trees from multiple alignments. We observe a drastic reduction of the efficiency of neighbor-joining even if the sequences are reasonably long. We also see that multiple alignment programs may force their implicit assumptions upon the sequences under study, thus being the cause of erroneous trees and erroneous support values.
Chapter 4 gives an introduction into the application of insertion and deletion models. These models are then used to simultaneously reconstruct phylogenies and multiple alignments (chapter 5). Finally, we describe in the appendices the usage and some implementation details of the main programs that were written for this thesis as well as some possible generalizations of the models applied.