https://github.com/ebedthan/darwin

Create (rapid) neighbor-joining tree from sequences using mash distance
https://github.com/ebedthan/darwin

Last synced: about 1 month ago
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Create (rapid) neighbor-joining tree from sequences using mash distance

• Host: GitHub
• URL: https://github.com/ebedthan/darwin
• Owner: Ebedthan
• License: mit
• Created: 2024-03-28T15:12:19.000Z (8 months ago)
• Default Branch: main
• Last Pushed: 2024-08-05T23:24:52.000Z (4 months ago)
• Last Synced: 2024-08-06T02:01:39.861Z (3 months ago)
• Language: Rust
• Homepage:
• Size: 10.3 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# darwin

[![Continuous Integration](https://github.com/Ebedthan/darwin/actions/workflows/ci.yml/badge.svg)](https://github.com/Ebedthan/darwin/actions/workflows/ci.yml)



    



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](https://github.com/onecodex/finch-rs) which is fast, have adaptive, count-based filtering (for FASTQs) and strandedness filtering. 

- Reliable and fast neighbor-joining tree estimation using [speedytree](https://docs.rs/speedytree/latest/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](https://www.rust-lang.org/) version is 1.74.1.

### Semver

`darwin` is following [Semantic Versioning 2.0](https://semver.org/).

### Licence

`darwin` is distributed under the terms of the MIT license.

See [LICENSE-MIT](https://github.com/Ebedthan/xgt/blob/main/LICENSE-MIT) for details.