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**   HHsuite for sensitive sequence searching version 3.0.0 (15-03-2015)   **
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 (C) Johannes Soeding, Markus Meier, Martin Steinegger, Michael Remmert, 
 Andreas Hauser, Andreas Biegert 2015

This README only serves as a quick start guide.
For full documentation see the user guide in hhsuite-userguide.pdf


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1. Requirements
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To compile from source, you will need:
 * a recent C/C++ compiler
 * CMake 2.8.12 or later
 * pdbx python library for example from https://github.com/soedinglab/pdbx

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2. Installation
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We recommend compiling HHsuite on the machine that should run the 
computations so that it can be optimized for the appropriate CPU architecture.

2.1 Packages

Some distributions incorporate HHsuite on their own:
* Ubuntu/Debian/etc. [DPKGs](http://packages.debian.org/source/sid/hhsuite) 
    are provided by Laszlo Kajan.
* For Archlinux you can find a PKGBUILD on aur 
    (https://aur.archlinux.org/packages/hhsuite/)

2.2 Release tarballs
 
The release tarballs (http://wwwuser.gwdg.de/~compbiol/data/hhsuite/releases/) 
should contain all required source files. Simply download and extract.


2.3 Cloning from GIT

If you want to compile the most recent version, simply clone the git 
repository. Then, from the repository root, initialize the ffindex submodule:

	git submodule init
	git submodule update


2.3.1 Compilation

With the sourcecode ready, simply run cmake with the default settings and 
libraries should be auto-detected:

	mkdir build
	cd build
	cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -G "Unix Makefiles" \\ 
	   -DCMAKE_INSTALL_PREFIX=${INSTALL_BASE_DIR} ..
	make
	make install


2.3.2 Setting environment variables

In your shell set environment variable HHLIB to ${INSTALL_BASE_DIR}, 
e.g (for bash, zsh, ksh):

	export HHLIB=${INSTALL_BASE_DIR}

HHsearch and HHblits look for the column state library file cs219.lib
and the context library file context_data.lib in ${HHLIB}/data/. The HHsuite
scripts also read HHLIB to locate the perl modules Align.pm and HHPaths.pm 
in ${HHLIB]/scripts/.  

Add the location of HHsuite binaries and scripts to your search PATH variable

	export PATH=${PATH}:${INSTALL_BASE_DIR}/bin:${INSTALL_BASE_DIR}/scripts


2.3.3 Specify BLAST, PSIPRED, PDB, DSSP paths

Specify paths in ${INSTALL_BASE_DIR}/scripts/HHPaths.pm where they are read
by HHsuite's perl scripts.


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3. Download Databases
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Download current databases from our server 
(http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/)
To build up multiple sequences alignments using HHblits uniprot20 is sufficient.


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4. Usage
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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>

You can get a detailed list of options for HHblits by running HHblits with 
the "-h" option.


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5. License
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The HHsearch/HHblits software package is distributed under Gnu Public Licence, 
Version 3. This means that the HH-suite 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.

This program is distributed in the hope that it will be useful, but WITHOUT 
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

See the copy of the GNU General Public License in the LICENSE file. 
If you do not have this file, see http://www.gnu.org/licenses/


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6. Notes
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For full documentation see the user guide in hhsuite-userguide.pdf

We are very grateful for bug reports! 
Please contact us at [email protected]


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7. Acknowledgements
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The hhsuite contains in file hhprefilter.cpp code adapted from Michael 
Farrar (http://sites.google.com/site/farrarmichael/smith-waterman). 
His code is marked in the file hhprefilter.cpp. For the copy right of that 
code, please see the LICENSE file that comes with HHsuite.
Reference: Farrar M. Striped Smith-Waterman speeds database searches six 
times over other SIMD implementations. Bioinformatics. 2007, 23:156-61.
Many posthumous thanks to Michael Farrar for his great code!