Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes - Supplementary Files S1-S5

Supplementary File S1: Simulation parameter
files and guide trees (ZIP archive)

Supplementary File S2: PCA plot based on
diversity of bi-allelic SNPs (PDF file). Same
projection as in Figure S5, with samples distinguished by different
metadata: country of isolation, year of isolation, host immune
status, body compartment of isolation ('respiratory' pools BAL and
nasal rinse, 'blood' pools whole blood and plasma).

Supplementary File S3: Posterior probability
and compatibility matrices of bipartitions in gene trees (XLSX
spreadsheet)

Supplementary File S4: Local LD index values
along HCMV whole-genome alignment. (XLSX spreadsheet)

Supplementary File S5: Trees of
hyper-variable loci with episodes of positive selection highlighted
(PDF file)