PhylogeneticTrees.jl

PhylogeneticTrees is a package implementing miqoGraph, a fast algorithm to fit admixture trees using mixed-integer quadratic optimization. It was developed using the Julia language and the Gurobi optimization solver.

Installation

PhylogeneticTrees is implemented using the Gurobi optimization solver, which has a free academic license. The instructions for installation can be found here.

The Julia language can be downloaded here. This package was developed using Julia 1.0.

PhylogeneticTrees can be installed through the Julia package manager:

(v1.0) pkg> add "https://github.com/juliayyan/PhylogeneticTrees.jl" 

To check that the installation is working properly, run the following within the package manager:

(v1.0) pkg> test PhylogeneticTrees

NOTE. The dependencies for PhylogeneticTrees include JuMP (v0.18.5), Gurobi, CSV (v0.4.3), DataFrames (v0.17.1), and LightGraphs. Newer or older versions of these packages may cause errors. To install a specific version of these packages, you can use the following commands:

(v1.0) pkg> add JuMP@0.18.5

(v1.0) pkg> add CSV@0.4.3

(v1.0) pkg> add DataFrames@0.17.1

Usage

Example code and datasets can be found in the test/ directory.

Citing PhylogeneticTrees

Our paper describing the models in this package can be found on bioRxiv. Documentation is in the supplementary material. If you find it useful in your work, we kindly request that you cite the following preprint:

@article{ypn2019,
  author = {Yan, Julia and Patterson, Nick and Narasimhan, Vagheesh},
  title = {miqoGraph: Fitting admixture graphs using mixed-integer quadratic optimization},
  elocation-id = {801548},
  year = {2019},
  doi = {10.1101/801548},
  publisher = {Cold Spring Harbor Laboratory},
  URL = {https://www.biorxiv.org/content/early/2019/10/11/801548},
  eprint = {https://www.biorxiv.org/content/early/2019/10/11/801548.full.pdf},
  journal = {bioRxiv}
}