Alignments are provided in Mega (*.meg) and Nexus (*.nex) format.  All trees were calculated excluding all sites with gaps, so all sites with gaps are removed from these alignments.
 

Figure 2 was based on an alignment of I homologs:

figure2meg.txt      figure2nex.txt

Figure 3 was based on an alignment of R homologs:

figure3meg.txt      figure3nex.txt

Figure 4 was based on a combined alignment of I and R homologs:

figure4meg.txt     figure4nex.txt
 

http://chuma.cas.usf.edu/~garey/alignments/gray&garey