darwin

darwin is a fast tool to build (rapid) neighbor-joining trees bases on mash distance. It takes as input the sequences (FASTA and FASTQ files are welcomed, compressed or not), compute the sketches and output a newick file of the tree.

The main advantages of darwin over others tools are:

• It uses the innovative approach of sketching algorithm finch which is fast, have adaptive, count-based filtering (for FASTQs) and strandedness filtering.
• Reliable and fast neighbor-joining tree estimation using speedytree.

darwin outputs the tree in newick format.

Quick start guide

# Compute rapid neighbor-joining tree of all files in a directory
darwin dir/*

# Compute rapid NJ tree using specific files
darwin file1.fa.gz file2.fq.xz file3.fna.bz2

# Compute canonical neighbor-joining tree
darwin -c dir/*

Full help is available from darwin --help;

Installation

git clone https://github.com/Ebedthan/darwin.git
cd darwin

# if default Rust install directory is ~/.cargo
cargo install --path . --root ~/.cargo
darwin -h

Minimum supported Rust version

darwin minimum Rust version is 1.74.1.

Semver

darwin is following Semantic Versioning 2.0.

Licence

darwin is distributed under the terms of the MIT license. See LICENSE-MIT for details.