thijsjanzen/nodeSub: Simulate DNA Alignments Using Node Substitutions

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. This 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:10.1093/sysbio/syab085>.

install.packages("remotes")
remotes::install_github("thijsjanzen/nodeSub")