#bioinformatics #rna #secondary-structure

bin+lib phyloalifold

PhyloAliFold Program, which Predicts RNA Consensus Secondary Structures to Incorporate Phylogeny among Homologs

4 releases

Uses old Rust 2015

0.1.3 Mar 10, 2020
0.1.2 Mar 9, 2020
0.1.1 Mar 9, 2020
0.1.0 Mar 4, 2020

#7 in #secondary-structure

42 downloads per month

MIT license

2.5MB
913 lines

PhyloAliFold Program, which Predicts RNA Consensus Secondary Structures to Incorporate Phylogeny among Homologs

Installation

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:

$ 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 RNA package to predict pairing probabilities by the RNAalipfold algorithm. Now you can install the PhyloAliFold program as follows:

$ cargo install phyloalifold

Check if this program has been installed properly as follows:

$ phyloalifold # Its available command options will be displayed.

After the test, the figures shown in the paper of the PhyloAliFold program can be reproduced:

$ cd src
$ ./run_all.py # Install python packages required to the reproduction. Saved figures will appear at the "../assets/images" directory.

Author

Heartsh

License

Copyright (c) 2018 Heartsh
Licensed under the MIT license.

Dependencies

~27MB
~200K SLoC