This will speed up species tree/network estimation in ~linear proportion to the number of CPUs available to you, if you are using the R package MSCquartets, by parallelising the quartetTable() funtion using future.apply.
R >= 3.2.0
R packages MSCquartets, future.apply
The recently developed R package MSCquartets (Rhodes et al. 2020) implements several algorithms for (network) multispecies coalescent-based species tree/network estimation, all of which seem to depend on the quartetTable() function, which loops over gene trees and counts quartet frequencies. The number of quartets for a given tree is n [choose] 4, which increases exponentially. The script here Parallel_quartetTable_byTree.R encodes Parallel_quartetTable_byTree() which uses the future.apply package to parallelise quartet counting by tree and then sums up the quartet frequencies to make a table identical to that generated by the original function. Parallel_NANUQ.R contains the aforementioned function and the function Parallel_NANUQ() which makes use of it (the internally called NANUQdist() function is unchanged).
RAM_Gigs=1 ; any real number, specifying the memory limit per core in gigabytes (for large trees, a lot of memory might be required; I've found 5 Gigs to work fine for <= 80-taxon trees)
parallel=TRUE (not available in Parallel_NANUQ()); if FALSE, it uses sapply() instead of future_sapply() which seems to actually be a little slower than the original function (not sure why)
https://cran.r-project.org/web/packages/MSCquartets/index.html https://cran.r-project.org/web/packages/future.apply/index.html
MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R John A. Rhodes, Hector Baños, Jonathan D. Mitchell, Elizabeth S. Allman bioRxiv 2020.05.01.073361; doi: https://doi.org/10.1101/2020.05.01.073361
Allman, E.S., Baños, H. & Rhodes, J.A. NANUQ: a method for inferring species networks from gene trees under the coalescent model. Algorithms Mol Biol 14, 24 (2019). https://doi.org/10.1186/s13015-019-0159-2
Bengtsson, H., 2018. future. apply: Apply function to elements in parallel using futures.