Accompanying data for the paper

This zip file contains sequence alignments (*.phyl) and phylogenetic trees (*.tree) for the PB2 and RBCL protein-coding genes analysed in the paper. It also contains estimates of fitness values at codon sites for the two proteins. The fitness estimates can be used to calculate the relative non-synonymous substitution rate as explained in the paper (e.g. Eq 3.1)

MakeTree.R

MakeTree.

PartitionAnalysisTimeMC.TableS1S2

Tables S1 & S

PartitionAnalysisTimeMC.FigS1

Figure S

RelClock.R

RelClock.

Supplementary Figure 1

Calibration vs. prior densities for strategies A and B. The dotted lines represent the calibration density, while the shaded (grey) histograms represent the effective prior obtained from MCMC sampling. Numbers in brackets indicate the 95% prior CI. Note that the priors for three Cauchy-based calibrations in strategy B (Primates, Anthropoidea and Human-Gorilla) have heavy tails that extend substantially back in time