DELINEATE: Species Delimitation¶
DELINEATE is a package that implements the DELINEATE approach to species delimitation (Sukumaran, Holder, and Knowles, 2020). This approach integrates an explicit model of speciation into the multipopulation coalescent (also known as the “censored” or “multispecies” coalescent) model, to organize a set of population lineages sampled from one or more species into mutually-exclusive and jointly-comprehensive subsets, where each subset of population lineages represents a distinct species.
DELINEATE requires Python 3.7 or greater to run. Package and dependency management is greatly simplified if pip is installed as well.
Providing you have all the system requirements (see the installation guide), you can use the following command to install or upgrade DELINEATE directly from the package repositories:
python3 -m pip install -U git+https://github.com/jeetsukumaran/delineate.git
- Basic Concepts
- Quick Start
- A Complete Worked Example: Lionepha
- (Software Prerequisites)
- (Data Files)
- Stage I: Identification of Population Units using the Multipopulation Coalescent Model
- Stage II. Generating the (Multipopulation Coalescent, Ultrametric) Phylogeny of Populations
- Stage III. Assignment of Known vs. Unknown Species Identities
- Stage IV. Delimitation of Species Units
- Examination and Interpretation of the Results