UC San Diego

In this dissertation, two problems are considered: phylogenetic reconstruction using micro-inversions as phylogenetic characters, and de novo fragment assembly of short reads. It is shown in Part 1 that one may use inversions at orthologous loci detected in pairwise alignments to reconstruct phylogeny. In Part 2, a method to assemble "short'', 30-100 base reads is presented. First, a study is shown that was the first to show that it is possible to perform de novo assembly of short (simulated) reads. Next, a method, EULER-SR is presented to assemble short reads produced by the 454 Life Sciences platform. Finally, the method EULER-USR is presented to perform mate-paired assembly of short, 35-50 base reads, and to perform error correction on reads with erroneous suffixes to recover a longer usable portion of an otherwise short read