rapidphylo is an R package for rapid estimation of tree-topology from large allele frequency data using Root Distances Method, under a Brownian Motion model. This is achieved by first computing the maximum likelihood estimates of the root distances, and then inferring the tree-topology from them.
Install the released version of this package from CRAN
install.packages("rapidphylo")Or install the development version of this package from GitHub
remotes::install_github('ArindamRoyChoudhury/rapidphylo', upgrade="never")# A dataset "Human_Allele_Frequencies" is loaded with the package;
# it has allele frequencies in 31,000 sites for 4 human populations and one outgroup human population.
# check data dimension
dim(Human_Allele_Frequencies)
# run RDM function
rd_tre <- RDM(Human_Allele_Frequencies, outgroup = "San", use = "pairwise.complete.obs")
# result visualization
plot(rd_tre, use.edge.length = FALSE, cex = 0.5)