Introduction

This is a Rust program designed to quickly generate many gene trees from a given species tree.

Installation

Building a project written in Rust is very easy.

1. Install the Cargo package manager.
2. Clone the repository.
3. Navigate inside the directory in the terminal.
4. Run the command cargo build --release. This will automatically download all necessary dependencies and compile the binary inside a new target directory.

Algorithm

This Rust script chooses a transfer uniformly along the branches of the trees, according to the model of gene transfers given by [ref].

Usage

Input:

1. A .nwk file containing a newick tree with node lengths and optional internal node names like so: ((a:1.0,b:1.0)c:1.0,d:2.0)e:0.0; The grammar for the parser, which you can easily modify to suit other formats of is defined in the newick.pest file. The parser is pest
2. The output directory out_dir.
3. The text file transfers_file containing the specified number of transfers to simulate for each gene tree, separated by commas and no blank spaces like 1,2,3,5.

Usage: ./gene_transfer_script <path_to_nwk_file> <output_directory> <path_to_transfers_file> <rng_seed>

Output: A new folder out_dir/tree_0 will be created, as well as out_dir/tree_0/genes and out_dir/tree_0/transfers, containing respectively the gene trees generated in newick format, and .csv files indicating the donor and receivers of simulated transfers, as well as the time of the transfers (starting from the root of the species tree). A gene tree out_dir/tree_0/genes/gene_{i}.nwk is created for each value in transfers_file, along with the csv file out_dir/tree_0/transfers/transfers_{i}.csv.