DeepMSA: multiple sequence alignment generation for protein structure prediction

==== Installing the package ====

This package is developed for 64bit Linux only. If you use 64bit Linux, you
should be able to use this package without compiling anything.

In theory, the package should also work for Mac OS, provided that you compile
the respective components appropriately. In particular, this package contains source code and/or binary executables from the following packages.

[1] hhsuite 2.0.16
    Source code and binaries included. Check "hhsuite-readme.txt" for
    compilation instruction.

[2] legacy BLAST 2.2.26
    Source code and binaries included. Check "ncbi-blast-legacy/README" for 
    compilation instruction.

[3] kClust 1.0
    Binaries included. Check https://github.com/soedinglab/kClust for source
    code.

[4] Clustal Omega 1.2.4
    Binary included. Check http://www.clustal.org/omega for source code.

[5] HMMER 3.1b2
    Modified binaries included. Check qhmmer/README to compile our modified
    source code for the qhmmsearch, qhmmbuild, and qjackhmmer binaries.

[6] MSAParser, our own program to calculate Nf.
    Binaries and source code include. To compile, run:
    $ cd MSAParser
    $ make
    $ make install

==== Running the package ====

The main program is "scripts/build_MSA.py". You can run the script without
any command line argument to get the help message.

==== License ====

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

If you find this program useful, please cite:

C Zhang, W Zheng, SM Mortuza, L Yang, Y Zhang (2019) DeepMSA: Deep multiple
sequence alignment generation for protein structure prediction. 
