"TreeSearch" is an R package that allows parsimony search on morphological datasets.
To use "TreeSearch" you will first need to install R. RStudio (overview) is a popular front-end that makes several of R's features easier to use.
The "TreeSearch" package can be installed as any other package. To get the latest stable version from CRAN, type
install.packages("TreeSearch")
into the R (or RStudio) command line.
Once installed, load the "TreeSearch" package into R using
library("TreeSearch")
Activate the graphical user interface by typing EasyTrees()
.
In Jan 2022, some users are reporting issues after loading trees from Nexus files. These arise due to an issue in the underlying "ape" package. To install a patched version, close and re-launch R and run:
if (!require("remotes")) install.packages("remotes") remotes::install_github("ms609/ape@patch-3")
Windows users may need to install Rtools before installing from the GitHub source.
To get the latest development version from GitHub, type
remotes::install_github("ms609/TreeSearch")
You might want to:
Load data from a Nexus file or spreadsheet
Conduct parsimony search using Brazeau, Guillerme & Smith's approach to inapplicable data, or using Profile parsimony.
Conduct parsimony search using custom optimality criteria.
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.