Alignments from Thornton, Bachtrog, and Andolfatto (2006) X-chromosomes and autosomes evolve at similar rates in Drosophila - no evidence for faster-X protein evolution. Genome Research 16: 498-504
Alignments and annotations from Thornton and Long (2005) Excess of Amino Acid Substitutions Relative to Polymorphism Between X-Linked Duplications in Drosophila melanogaster. Mol. Biol. Evol. 22: 273-284. This contains the alignments used for summary statistics, and the annotation files compatible with "polydNdS" in my analysis software package. It currently does not contain the files used for McDonald-Kreitman tests, or the analysis of gene conversion between paralogs. For the moment, those are available on request to Kevin Thornton.
Simulation source code and output from Thornton, Foran, and Long (2013) Properties and Modeling of GWAS when Complex Disease Risk is due to non-complementing, deleterious mutations in genes of large effect. PLoS Genetics 9: e1003258