This repository contains a rust crate to compute the cophenetic distance between two rooted phylogenetic trees in near-linear time.

To install you must first have cargo and rustup installed:

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

After installing the above command you can run the following to install nlcd:

cargo install --git=https://github.com/sriram98v/near-linear-cophenetic-distance

Alternatively, you can install seq_class by cloning this repository and building it locally:

git clone https://github.com/sriram98v/near-linear-cophenetic-distance
cd near-linear-cophenetic-distance
cargo install --path=./

To compute the cophenetic distance between a pair of trees, please create a single file with the extension .tre containing the two trees in Newick format (line-separated). The run the following command to compute the cophenetic distance with depth as the path function:

nlcd dist -i <PATH TO .TRE FILE> -p <NORM>

Please refer the help page for details on how to use other path functions using:

nlcd -h

In order to reproduce the results as seen in the article, run the following command

nlcd repr-emp -n 1000 -x 100 -p 10 -t 1 -o ./emp-study

In order to plot the results, create a local python virtual environment and install the dependencies using the following commands:

python3 -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

The command above will create a file containing the distributions as seen in the Results section of the article. In order to reproduce the plots, please run the python script provided in the scripts directory as follows (run from the base of the repository):

./scripts/plot-distribs.py

Note: Reproduction of these results may not looked identical to that in the aritcle In order to reproduce the scalability analysis as seen in the article, run the following command

nlcd repr-sca -s 200 -e 10000 -x 200 -i 20 -p 5 -o ./sca-study

In order to plot the results, create a local python virtual environment and install the dependencies using the following commands:

python3 -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

The command above will create a file containing the distributions as seen in the Results section of the article. In order to reproduce the plots, please run the python script provided in the scripts directory as follows (run from the base of the repository):

./scripts/plot-sca.py