cedar

🗺️ Overview

cedar 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 cedar 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.

cedar outputs the tree in newick format.

🔧 Installing

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

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

💡 Examples

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

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

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

Full help is available from cedar --help;

Minimum supported Rust version

cedar minimum Rust version is 1.74.1.

Semver

cedar is following Semantic Versioning 2.0.

Licence

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