https://github.com/ebedthan/darwin
Create (rapid) neighbor-joining tree from sequences using mash distance
https://github.com/ebedthan/darwin
Last synced: 3 months 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 (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-01-29T18:08:53.000Z (4 months ago)
- Last Synced: 2025-01-29T19:21:23.221Z (4 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
## 🗺️ Overview
`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.
## 🔧 Installing
```
git clone https://github.com/Ebedthan/darwin.git
cd darwin
# if default Rust install directory is ~/.cargo
cargo install --path . --root ~/.cargo
darwin -h
```
## 💡 Examples
```
# 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`;
### 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.