• Allowing for non-contemporary samples, e.g., ancient DNA: Simply add the --sample_ages option.
• Allowing for haploid organisms: set the ID_2 column in the sample file to NA and Relate will work for haploid organisms.
• Improved coalescence rate estimation: The algorithm has been improved and behaviour has changed slightly. The output now always contains all trees, and the threshold parameter only affects iterations leading up to the last one. The threshold parameter now is a float in [0,1], specifying the proportion of trees to throw away (Default = 0.5).
• Arbitrary strings as chromosome IDs: in scripts such as EstimatePopulationSize.sh, use the --chr option to specify a file containing chromosome name.
• More flexible epochs for coalescence rate estimation: use the option --bins to specify epoch boundaries in the format 10^seq(x,y,stepsize).

We deposited Relate-estimated coalescence rates, allele ages, and p-values for evidence of positive selection for the 1000 Genomes Project here.
These were obtained by estimating the joint genealogy of all 1000 GP populations and then extracted the embedded genealogy for each population. For the genealogy of each population, we jointly estimated the population size history and branch lengths. Variants segregating in more than one population therefore have correlated but different allele ages in each population.

I made an R package for handling Relate output files (MIT license). It's still under development but the main functionality is working.

library(devtools)
devtools::install_github("leospeidel/relater")

This github repo contains functions to convert between Relate and tskit format (MIT license).

It doubles as a C++ library you can link to if you want to use some of our Relate functions in C++.

relate_lib/bin/Convert --mode ConvertFromTreeSequence \
		--anc example.anc.gz \
		--mut example.mut.gz \
		-i example

relate_lib/bin/Convert --mode ConvertToTreeSequence \
		--anc example.anc.gz \
		--mut example.mut.gz \
		-o example

Thanks to Nathaniel S. Pope, you can now also specify an argument that compresses these Relate-converted tree sequences by assigning the same age to nodes with identical descendant sets across adjacent trees.

relate_lib/bin/Convert --mode ConvertToTreeSequence \
		--compress \
		--anc example.anc.gz \
		--mut example.mut.gz \
		-o example