The following is a list of papers that are relevant to the Drosophila 12 Genomes project that are a good starting point for understanding the data.

SCHAEFFER, S. W., A. BHUTKAR, B. F. MCALLISTER, M. MATSUDA, L. M. MATZKIN et al., 2008 Polytene chromosomal maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps. Genetics 179: 1601-1655.  This paper describes how the genome scaffolds were mapped to the polytene chromosomes.  The Drosophila system provides an excellent system to validate the locations of the individual scaffolds from the genome project.

BHUTKAR, A., S. W. SCHAEFFER, S. RUSSO, M. XU, T. F. SMITH et al., 2008 Chromosomal rearrangement inferred from comparisons of twelve Drosophila genomes. Genetics 179: 1657-1680. This paper used the mapped scaffolds to infer the rates of rearrangements for the 12 genomes using a variety of approaches including linkage chain analysis, which was developed by S. W. Schaeffer.

Combinatorics of Genome Rearrangements (Computational Molecular Biology)

by Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier and, Stephane Vialette

Reviews (copied from Amazon):

“Combinatorics of Genome Rearrangement is the first computer science monograph on this rapidly expanding field. The authors have managed the seemingly impossible feat of combining scope and coherence; they have pulled together all the disparate research lines and integrated them through a common treatment and notation. This volume is simultaneously an accessible computational biology textbook for computer science and bioinformatics students, an easy and thorough entry to the field for professionals attracted by the novelty and diversity of the problems in the field, and an up-to-date reference book for specialists.”
—David Sankoff, Department of Mathematics and Statistics, University of Ottawa

“This book will be a defining book for the field of genome rearrangement and is destined to become a classic as soon as it hits the bookshelves. The authors have done an excellent job in presenting one of the most technically challenging areas of computational biology in an easily understood manner. Dobzhansky and Sturtevant would not be disappointed.”
—Pavel Pevzner, Ronald R. Taylor Chair of Computer Science, Director, Interdisciplinary Bioinformatics Program, University of California, San Diego