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 Binaries included. Check ncbi-blast-legacy for source code and ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ for binary executable.
[3] kClust 1.0 Binaries included. Check kClust for source code.
[4] Clustal Omega 1.2.4 Binary included. Check CLustal Omega for source code.
[5] HMMER 3.1b2 Modified binaries included. Check qhmmer to compile our modified source code for the qhmmsearch, qhmmbuild, and qjackhmmer binaries.
[6] MSAParser, our own program to calculate Nf. Check https://github.com/kad-ecoli/MSAParser/ for source code.
The main program is scripts/build_MSA.py. You can run the script without any command line argument to get the help message. The program needs python2.7; python3 will result in error.
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: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinformatics. DOI: 10.1093/bioinformatics/btz863