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Code contains all Matlab functions required to run the code described in the paper.

Bone5 contains methylation values in the Bone 5 reference. The file should be unzipped and then used in RoAM.
CpG coordinates is the pickled python object that contains the coordinates of the CpG position in hg19.

The data contains the genotype information (*.geno), as well the accompanying information on the individuals (*.ind) and SNPs (*.snp).

Big Excel tables that are referred to in the thesis.

The data comprises the full reconstructed methylated (as β-values) along the entire Neandertal and the Denisovan genomes.