1 Changes from Version 0

Everything that was possible with Version 0 is still possible now. The main difference is that we now provide a single interface, ‘fs’, to access all functions and to make managing the computational pipeline much easier. Specifically, this code incorporates:

• ChromoPainter: Taking in phased sequence data, this ‘paints’ each haplotype using the others.
• ChromoCombine: This combines the output of ChromoPainter into a few files summarizing the genome-wide sharing of haplotypes between all individuals. The main output of chromocombibe is the ‘coancestry matrix’.
• FineSTRUCTURE: Working with the coancestry matrix, we identify statistically indistinguishable individuals and cluster them.

We have added diagnostic tests for MCMC convergence to ensure that FineSTRUCTURE has been run long enough.

If you have only a small dataset, then you can run the entire pipeline, exploiting multiple processors, using a single command. If you have a large dataset and a HPC machine, it can instead provide command lines to be processed.