Alternatives to PSMC

PSMC is my program to infer the historical effective population size from a diploid genome. It was published in Nature three years ago and has been cited over 100 times so far. Whenever I see a PSMC plot in a paper, I feel a moment of joy both as a scientist and as a programmer.

PSMC is okay, but now there are better models and implementations at least in theory. MSMC, which has recently been published in Nature Genetics, not only extends PSMC to multiple haplotypes, but also improves PSMC for a diploid genome. It precalculates transition matrices over long runs of homozygosity and becomes fast enough to perform whole-genome inference without binning the input like PSMC. More importantly, for a diploid genome, MSMC implements the PSMC’ model. It is a better approximation to the coalescent-with-recombination model by allowing non-effective recombinations. It is able to give a much better estimate of the recombination rate. I was lazy when I was working on PSMC. I knew PSMC’ is better, but I skipped that because its derivation is more complicated and because PSMC worked well to infer other parameters.

Another important tool is dical by Kelly Harris et al. It also uses better model and has a time complexity linear in the number of states. This is a significant advantage over the PSMC implementation whose time complexity is quadratic in the number of states. Dical runs much faster.

You can still use PSMC if you prefer. It comes with a few useful scripts and is fast enough for most applications. Just beware that there may be better ones when PSMC is not for you.