Phylo2Vec: a vector representation for binary trees

Installation

Prerequisites:

• C++14
• GoogleTest 1.11.0: sudo apt-get install libgtest-dev
• clang-format: sudo apt install clang-format
• cmake 3.22.1: sudo apt-get install cmake
• cxxopts 3.1.1:

  git clone https://github.com/jarro2783/cxxopts.git
  cd cxxopts
  mkdir build
  cd build
  cmake ..
  make
  sudo make install
  

Compile and build from scratch:

mkdir build
cd build
cmake ..
make

Or use the executable. To get information about all arguments:

./phylo2vec -h

Arguments:

  -h, --help            Show help
      --toNewick arg    Convert to Newick format. Example input: 0 1 4
      --toVector arg    Convert to integer vector. Example input:
                        "(((2,1)4,0)5,3)6;"
      --with_mapping    For Newicks that do not only contain digits, to use with toVector. Example input: "(((((((tip_0:1.44,tip_1:1.44)8042:0.46,(tip_2:1.5,tip_3:1.5)8043:0.4)8044:0.3,(tip_4:1.51,tip_5:1.51)8045:0.69)8046:0.4,tip_6:2.6)8047:1.05,tip_7:3.65)8048:0.5,(((tip_8:0.72,tip_9:0.72)8049:0.28,tip_10:1)8050:1.56,tip_11:2.56)8051:1.59)8052:1.96,tip_12:6.11)8053:0;"
      --num_leaves arg  Number of leaves (optional, but recommended when
                        using toVector)

Example usage of toNewick:

phylo2vec --toNewick 0 1 4

Example usage of toVector:

phylo2vec --toVector "(((2,1)4,0)5,3)6;" --num_leaves 4

Example usage of toVector:

./phylo2vec --with_mapping --toVector "(((((((tip_0:1.44,tip_1:1.44)8042:0.46,(tip_2:1.5,tip_3:1.5)8043:0.4)8044:0.3,(tip_4:1.51,tip_5:1.51)8045:0.69)8046:0.4,tip_6:2.6)8047:1.05,tip_7:3.65)8048:0.5,(((tip_8:0.72,tip_9:0.72)8049:0.28,tip_10:1)8050:1.56,tip_11:2.56)8051:1.59)8052:1.96,tip_12:6.11)8053:0;"

Python version:

• https://github.com/Neclow/phylo2vec written with Matthew Penn and Samir Bhatt
• A minimalistic demo is available on Colab:

Citation and other work

• Link to the preprint: https://arxiv.org/abs/2304.12693
• Related work: https://github.com/Neclow/GradME = phylo2vec + minimum evolution + gradient descent
• The file 100trees.txt is an anonmyised subset of TimeTree trees adapted from: https://datadryad.org/stash/dataset/doi:10.5061/dryad.2fqz612vg. Kudos to Mark Khurana for the dataset

Note

• At least half of this repo was coded on a Samsung A40 using JDoodle, that should probably deserve a star :)