Preface

Since the identification of DNA/RNA as genetic material, deciphering the code of life has been a major goal put forward by biologists. One approach particularly successful in studying DNA sequences is to compare related sequences from different organisms. Se-quence alignment, specifically pairwise alignment, is among the earliest tool developed in bioinformatics. However, the generalization of pairwise alignment to multiple sequence alignment is not straightforward. The comparison of multiple sequences is expressed in two different but related problems: multiple sequence alignment finding shared homologous regions among input sequences, and phylogeny inference finding the order by which each sequence diverges from a common parent. These two problems have been under intensive research in the last three decades. However, multiple sequence alignment and phylogeny inference are not completely solved problems, in the sense that there is no single best algorithm that stands out practically and theoretically for each of these problems. My first encounter of the phylogeny inference problem was in 2010, when Prof. Ken Sung at the National University of Singapore gave us an assignment to infer the phylogen