nail

About

nail is a biological sequence alignment tool. Currently, only protein sequence alignment is supported.

nail uses 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.

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