(C) Johannes Soeding, Markus Meier, Martin Steinegger, Milot, Mirdita, Michael Remmert, Andreas Hauser, Andreas Biegert
The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
We provide an extensive user guide with many usage examples, frequently asked questions and guides to build your own databases.
We recommend compiling HH-suite on the machine that should run the computations so that it can be optimized for the available CPU instruction sets.
To compile from source, you will need a recent C/C++ compiler (at least GCC 4.8 or Clang 3.6) and CMake 2.8.12 or later.
To download the source code and compile the HH-suite execute the following commands:
git clone https://github.com/soedinglab/hh-suite.git
cd hh-suite && mkdir build && cd build
cmake -DCMAKE_INSTALL_PREFIX=. ..
make -j 4 && make install
export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"
Download current databases from our download server. To build up multiple sequences alignments using HHblits, the Uniclust30 database is sufficient.
For performing a single search iteration of HHblits, run HHblits with the following command:
hhblits -i <input-file> -o <result-file> -n 1 -d <database-basename>
For generating an alignment of homologous sequences:
hhblits -i <input-file> -o <result-file> -oa3m <result-alignment> -d <database-basename>
A detailed list of options for HHblits is available by running HHblits with the -h parameter.
Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger S J, and Söding J (2019) HH-suite3 for fast remote homology detection and deep protein annotation, bioRxiv, 560029. doi: 10.1101/560029