These are the alignments used in the paper by Bazykin and Kondrashov 
"Major role of positive selection in evolution of conservative segments of 
Drosophila proteins" (Proc Biol Sci. 2012 279(1742):3409-17).

The format is a multiple FASTA, concatenated for 13300 genes. 
For each gene, the following 177 sequences are given:
15 insect species;
162 Dmel sequences from Trudy Mackay's lab;
consensus of 162 D. melanogaster sequences.

Species are named as in UCSC Genome Browser. "@" means no alignment for this region, "-" means gap in alignment.