Many of the analyses reported in the paper were based on the six data sets given here. (You can also find them under Shared Data -> Data LIbraries -> Genome Diversity, then under aye-aye and human.)
The first data set contains 4,555,737 putative aye-aye SNPs, each recorded in a row with 59 columns.
The second data set contains 19,670 aye-aye "SAPs", i.e., Single Amino-acid Polymorphisms, including synonymous coding-region substitutions, each recorded in a row with 9 columns.
For estimating diversity within populations, we need to know which protein-coding positions are covered by sufficiently many reads that we should be able to identify any SNP. We put this information in a table having 8 columns.
For each of the above three tables for the aye-aye, we have closely analogous tables for matched data sets for 12 human individuals. The SNP table has 8,598,051 entries, each with 53 columns.
There are 50,475 human SAPs, each with 7 columns.
The table of adequately covered human coding intervals has 5 columns.
The workflows contain commands for the main analyses reported in the body of the paper. The user is invited to modify the commands to compute more of the results described in the main paper and supplement. Many of the Galaxy tools used in these workflows can be found under "Genome Diversity" in the left panel on the Analyze Data page. A tutorial can be found under Example 4 on this page.
The first workflow creates the data for Figure 2, as well as a plot of distributions of coverage depth at each SNP for the 13 individuals (including North5, which we left out of other analyses because of low coverage). The workflow needs to be applied to the "aye-aye SNPs" data set as follows: (1) Under "Analyze Data" (in the black bar) create an empty history. (2) Under "Shared Data" -> "Published Pages", view this page. (3) Import the "aye-aye SNPs" data set ("+" in the green circle near the right of the green bar), then click on "return to the previous page". (4) Import the "aye-aye Figure 2" workflow, and click on "start using this workflow". (5) You will be taken to your Workflow page, which will have a workflow called "imported aye-aye Figure 2"; click on it and select "run". (6) You will be taken to a history that includes the aye-aye SNPs and the aye-aye Figure 2 workflow; scroll to the bottom of the workflow (middle panel) and press "Run workflow". The commands will take a couple of minutes to run.
The second workflow performs the basic analysis behind Figure 3, yielding Fst estimations for both North-vs-East aye-ayes and European-vs-African humans. It uses both the aye-aye and human SNP data sets.
The final workflow estimates the diversity parameter pi for North aye-ayes and European humans. It uses all six of the data sets listed above.