RPANDA, nLTT, apTreeshape, phangorn, tibble, DDD, Rmpfr,
assertthat, pbapply, phylobase, geiger, ape, babette, beautier,
beastier, mauricer, tracerer, rappdirs, testit, stringr

apTreeshape, phangorn, tibble, DDD, Rmpfr, assertthat,
pbapply, phylobase, geiger, babette, beautier, beastier,
mauricer, tracerer, rappdirs, testit, stringr
testthat, TreeSim, dplyr, knitr, rmarkdown, ggplot2,
magrittr, tidyr

testthat, TreeSim, dplyr, knitr, rmarkdown, ggplot2,
magrittr, tidyr, nLTT, RPANDA

Simulate DNA sequences for the node substitution model.
In the node substitution model, substitutions accumulate additionally
during a speciation event, providing a potential mechanistic explanation for
substitution rate variation. The nodeSub package provides tools to simulate
such a process, simulate a reference process with only substitutions along
the branches, and provides tools to infer phylogenies from alignments. More
information can be found in Janzen (2021) <doi:10.1101/2020.08.19.256891>.
nLTT, RPANDA, apTreeshape, phangorn, tibble, DDD, Rmpfr,
assertthat, pbapply, phylobase, rappdirs, stringr, geiger, ape,
testit, babette, beautier, beastier, mauricer, tracerer

Compares the distribution of sister clades through a phylogeny
An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution). DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
R (>= 3.0), picante, raster, ape, sp, vegan

Compares the Distribution of Sister Clades Through a Phylogeny

An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.