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https://github.com/soedinglab/hh-suite

Remote protein homology detection suite.
https://github.com/soedinglab/hh-suite

alignment bioinformatics cpp hh-suite hhblits hhpred hhsearch opensource profile-profile-search profile-search protein-structure sequence-search simd viterbi

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Remote protein homology detection suite.

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README 

        
# HH-suite3 for sensitive sequence searching



(C) Johannes Soeding, Markus Meier, Martin Steinegger, Milot Mirdita, Michael Remmert, Andreas Hauser, Andreas Biegert



[![BioConda Install](https://img.shields.io/conda/dn/bioconda/hhsuite.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/hhsuite)

[![Biocontainer Pulls](https://img.shields.io/endpoint?url=https%3A%2F%2Fmmseqs.com%2Fbiocontainer.php%3Fcontainer%3Dhhsuite)](https://biocontainers.pro/#/tools/hhsuite)

[![Github All Releases](https://img.shields.io/github/downloads/soedinglab/hh-suite/total.svg)](https://github.com/soedinglab/hh-suite/releases/latest)

[![Docker Pulls](https://img.shields.io/docker/pulls/soedinglab/hh-suite.svg)](https://hub.docker.com/r/soedinglab/hh-suite)

[![Build Status](https://dev.azure.com/themartinsteinegger/hhsuite/_apis/build/status/soedinglab.hh-suite?branchName=master)](https://dev.azure.com/themartinsteinegger/hhsuite/_build/latest?definitionId=4&branchName=master)



The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).



## Documentation



We provide an extensive [user guide](https://github.com/soedinglab/hh-suite/wiki) with many usage examples, frequently asked questions and guides to build your own databases. 



### Installation



HH-suite3 can also be installed by downloading a statically compiled version, [conda](https://github.com/conda/conda) or [Docker](https://github.com/moby/moby). HH-suite3 requires a 64-bit system (check with `uname -a | grep x86_64`). On AMD/Intel CPUs it requires at least support for the SSE2 instruction set (check by executing `cat /proc/cpuinfo | grep sse2` on Linux or `sysctl -a | grep machdep.cpu.features | grep SSE2` on macOS). `AVX2` is roughly 2x faster compared to SSE2. HH-suite3 also works on Linux systems with ARM64 and PPC64LE CPUs. Precompiled binaries for all supported systems can be found at [mmseqs.com/hhsuite](https://mmseqs.com/hhsuite).



```

# install via conda

conda install -c conda-forge -c bioconda hhsuite 

# install docker

docker pull soedinglab/hh-suite

# static SSE2 build

wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-SSE2-Linux.tar.gz; tar xvfz hhsuite-3.3.0-SSE2-Linux.tar.gz; export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"

# static AVX2 build

wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz; tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz; export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"

```

:exclamation: Only the self-compiled HH-suite3 version includes MPI support, since MPI configuration is specific to the local environment.



### Available Databases

List of available database for HH-suite3: 

  - [Uniclust30](https://uniclust.mmseqs.com) [[pub]](https://doi.org/10.1093/nar/gkw1081)

  - [BFD](https://bfd.mmseqs.com) (consists of 2.5 billion, mostly enviromental, protein sequences) [[pub]](https://doi.org/10.1038/s41592-019-0437-4)

  - [Pfam/SCOP/PDB70/dbCAN](http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/)



Also checkout the [databases (COG/ECOG/CD/...)](http://ftp.tuebingen.mpg.de/pub/protevo/toolkit/databases/hhsuite_dbs) maintained by the [MPI Bioinformatics Toolkit](https://toolkit.tuebingen.mpg.de) [[pub]](https://doi.org/10.1002/cpbi.108).



### Compilation

To compile from source, you will need a recent C/C++ compiler (at least GCC 4.8 or Clang 3.6) and [CMake](http://cmake.org/) 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

mkdir -p hh-suite/build && cd hh-suite/build

cmake -DCMAKE_INSTALL_PREFIX=. ..

make -j 4 && make install

export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"

```



:exclamation: To compile HH-suite3 on macOS, first install the `gcc` compiler from [Homebrew](https://brew.sh). The default macOS `clang` compiler does not support OpenMP and HH-suite3 will only be able to use a single thread. Then replace the `cmake` call above with the following one:



```

CC="$(brew --prefix)/bin/gcc-10" CXX="$(brew --prefix)/bin/g++-10" cmake -DCMAKE_INSTALL_PREFIX=. ..

```    



## Usage

For performing a single search iteration of HHblits, run HHblits with the following command:

```

hhblits -i  -o  -n 1 -d 

```



For generating an alignment of homologous sequences:

```

hhblits -i  -o  -oa3m  -d 

```



A detailed list of options for HHblits is available by running HHblits with the `-h` parameter.



## Reference



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, *BMC Bioinformatics*, 473. [doi: 10.1186/s12859-019-3019-7](https://doi.org/10.1186/s12859-019-3019-7)



## Links



* [Soeding lab](http://www.mpibpc.mpg.de/soeding)

* [Databases for the HH-suite](http://wwwuser.gwdg.de/~compbiol/data/hhsuite/)