This project provides the NeoAliFold Program, a program for the maximum-expected-accuracy estimations of RNA consensus secondary structures.
This project has been written in mainly Rust, a systems programming language.
So first, you need to install the Rust compiler, package manager, and standard library.
Visit the Rust website to see more about this language.
You can install these 3 components with 1 line as follows:
bash
$ curl https://sh.rustup.rs -sSf | sh
The above installation is done by Rustup, so you can easily switch a compiler to use.
Also you need to install the Centroid package to predict pairing probabilities by the RNAalipfold algorithm.
Now you can install the PhyloAliFold program and its dependent, the PhyloProb program, as follows:
bash
$ cargo install phyloprob # You input the probabilities computed by this program to "phylofold"
$ cargo install phyloalifold
Check if this program has been installed properly as follows:
bash
$ phyloprob
$ phyloalifold
After the test, the figures shown in the paper of the PhyloFold program can be reproduced:
bash
$ cd src
$ ./run_all.py # Install python packages required to the reproduction. Saved figures will appear at the "../assets/images" directory.
Copyright (c) 2018 Heartsh
Licensed under the MIT license.