The R package treestructure contains function to detect population structure from the history of coalescent events recorded in phylogenetic trees. This method classifies each tip and internal node of a tree into disjoint sets characterized by similar coalescent patterns.
It also possible to use node support values (i.e. bootstrap values) to avoid designating population structure in badly supported clades.
Installation
# You will need to install the R package devtools
# (https://github.com/r-lib/devtools)
install.packages("devtools")
devtools::install_github("emvolz-phylodynamics/treestructure")Alternatively, you can download this repository from here and follow instructions for your OS on installing packages from source.
We also provide a command-line interface for treestructure. See inst/tscl. If you would like to use the command-line interface you will need to install the R package getopt.
You can then use the flag -h for how to use the treestructure command-line interface direct in a terminal.
Tutorials
We recommend that you read the Get started to understand the basic functions in
treestructure.For an additional tutorial on how to include branch support to avoid designating population structure in badly supported clades, see this example for SARS-CoV-2.
Author
treestructure has been developed by Erik Volz.
Citation
Erik Volz, Wiuf Carsten, Yonatan Grad, Simon Frost, Ann Dennis, Xavier Didelot, (2020); Identification of hidden population structure in time-scaled phylogenies; Systemantic Biology, 69: 884–896.