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.