# nail
## About
nail is a biological sequence alignment tool. Currently, only protein sequence alignment is supported.
nail uses [MMseqs2](https://github.com/soedinglab/MMseqs2) to find rough alignment seeds to use as a starting point
for a highly sensitive, bounded sequence alignment algorithm.
## Installation
To build nail from source, you'll first need to install Rust and Cargo.
The easiest way to do that is to use [rustup](https://rustup.rs/).
Once that's done, you can then build nail:
git clone https://github.com/TravisWheelerLab/nail
cd nail/
cargo build --release
You'll then find the compiled binary at: `target/release/nail`
For example, try running:
target/release/nail -h
## Usage
The input to nail is a query multiple sequence alignment (stockholm) file and a target sequence (fasta) file.
To run the nail pipeline, use the `nail search` command:
For example:
$ nail search query.sto target.fa
## License
nail is licensed under the BSD-3-Clause license.
See `LICENSE` for details.
## Authors
Jack Roddy - jroddy@arizona.edu