This is the Git repository containing all code and simulation data for the paper titled "A two-state model of tree evolution and its applications to Alu retrotransposition" (doi:10.1093/sysbio/syx088). The supplementary files for the paper can be found here.

NOTE: If you want to sample trees under the dual-birth, DO NOT use the simulator in this repository! The original algorithm proposed in the paper is O(n log n) for a tree with n leaves, but we more recently proposed a O(n) algorithm that we proved correct and implemented in C++ ("A linear-time algorithm to sample the dual-birth model", doi:10.1101/226423), which can be found here. The original implementation is being kept here for the sake of reproducibility of the original paper.

• Python Modules
  • DendroPy
  • matplotlib
  • NumPy
  • SciPy
  • Seaborn
• Software
  • My tools repository (numlist, specifically)
  • FastTree
  • INDELible
  • RAxML

• tools: The tools we developed in this paper
• helper-scripts: Small scripts that helped automate various tasks