Provider Identification

The following provides mandatory data concerning the provider of this website, obligations with regard to data protection, as well as other important legal references involving the Internet site of the MPI Bioinformatics Toolkit ( as required by German law.


The provider of this Internet site within the legal meaning of the term is the registered association Max Planck Society for the Advancement of Science e.V..


Max-Planck-Gesellschaft zur Foerderung der Wissenschaften e.V.
Hofgartenstrasse 8
80539 Munich
Phone: +49 89 2108-0

Register of Societies and Associations

The Max Planck Society is registered in the Official Register of Societies and Associations at Berlin-Charlottenburg Local Court under the register number VR 13378 B.


The Max Planck Society is legally represented by its Board of Directors which, in turn, is represented by the President of the Society, Prof. Dr. Martin Stratmann and by Secretary General Dr. Ludwig Kronthaler.

Value Added Tax Identification Number

The value added tax identification number of the Max Planck Society is DE 129517720.


Responsible editors for the contents of the website of the MPI Bioinformatics Toolkit ( with regard to media law:

Dr. Vikram Alva Kullanja
MPI for Developmental Biology
Spemannstr. 35
72076 Tübingen

Legal Structure

The Max Planck Society is a non-profit research facility which is organized as a registered association. All of the institutes and facilities of the Max Planck Society are largely autonomous in terms of organization and research, but as a rule have no legal capacity of their own.

Foreign Language Pages

To the extent that parts of this Internet site are offered in languages other than German, this represents a service exclusively for staff and guests of the Max Planck Society who are not proficient in German.

Liability for Contents of Online Information

As the provider of contents in accordance with Section 7 Paragraph 1 of the Tele-Media Law, the Max Planck Society shall be responsible for any contents which it makes available for use in accordance with general legal provisions. The Max Planck Society makes every effort to provide timely and accurate information on this Web site. Nevertheless, errors and inaccuracies cannot be completely ruled out. Therefore, the Max Planck Society does not assume any liability for the relevance, accuracy, completeness or quality of the information provided. The Max Planck Society shall not be liable for damage of a tangible or intangible nature caused directly or indirectly through the use or failure to use the information offered and/or through the use of faulty or incomplete information unless it is verifiably culpable of intent or gross negligence. The same shall apply to any downloadable software available free of charge. The Max Planck Society reserves the right to modify, supplement, or delete any or all of the information offered on its Internet site, or to temporarily or permanently cease publication thereof without prior and separate notification.

Links to Internet Sites of Third Parties

This Internet site includes links to external pages.

The respective provider shall be responsible for the contents of any linked external pages. In establishing the initial link, the Max Planck Society has reviewed the respective external content in order to determine whether such link entailed possible civilor criminal responsibility. However, a constant review of linked external pages is unreasonable without concrete reason to believe that a violation of the law may be involved. If the Max Planck Society determines such or it is pointed out by others that an external offer to which it is connected via a link entails civil or criminal responsibility, then the Max Planck Society will immediately eliminate any link to this offer. The Max Planck Society expressly dissociates itself from such contents.


The layout, graphics employed and any other contents on the homepage of the Max Planck Society Internet site are protected by copyright law.
© Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V., Munich. All rights reserved

Privacy Policy

Data Collection and Processing

We wish to make our websites as appealing and comfortable for you as possible. To this end, analysis of statistical information relating to your utilisation of our websites and the collection of technical details on the web browsers and computers of our online visitors is very helpful for us.
We must advise you, however, that your IP address and perhaps other data related to your person will be transmitted to the service provider concerned and may be stored or analyzed there.

The data protection officer of the Max Planck Society is available for questions concerning the topic of data protection at dsb[at] or +49 89 2108-1554.

Personalized Services / Newsletter

Insofar as you have decided to take advantage of a personalized service such as registering an account, subscribing to newsletter services or completing contact forms, the required personal data are stored.
As a rule, this includes your e-mail address, first and surname, as well as other data – depending on the type of offer. Your data are used only in order to provide you with the desired offer to your satisfaction and in order to respond to any inquiries. If you no longer wish to take advantage of a personalized service, your personal data will be deleted after you cancel your registration.

Data Transmission

Your personal data will only be transmitted to government organizations and authorities in legally required cases and/or for prosecution in the event of attacks on our network infrastructure. Your personal data are not provided to third parties for any other purpose.

Data Collection Declaration

Insofar as you have not objected, the following data are being recorded by our central server and included in the usage statistics.

Basic data:
  • IP address, shortened for anonymity
  • A cookie to distinguish different visitors
  • The previously visited URL (referrer), insofar as it has been transmitted by your browser
  • Name and version of your operating system
  • Name, version and language settings of your browser
Additional data, if JavaScript is active:
  • URLs visited in this website
  • Time stamps of visits
  • Types of HTML requests
  • Screen resolution and colour depth
  • Technical processes and formats supported by your browser (e.g. cookies, Java, Flash, PDF, WindowsMedia, QuickTime, RealPlayer, Director, SilverLight, Google Gears)
Application log files

For technical reasons, our servers and applications save personal details upon your visit to our websites in their log files. However, these data are only used for the immediate provision of our services, for troubleshooting purposes or for attack prevention and are deleted automatically after a short period of time.

The following data are saved temporarily:
  • Your IP address
  • Date and time of your website visit
  • The address of the website visited
  • The address of the previously visited website (referrer)
  • Name and version of your browser / operating system (insofar as it has been transmitted by your browser)
  • Your E-mail address (e.g. when using the contact form)
Contact Us

Send your feature requests, comments or bug reports to:

Please contact the Södinglab regarding issues pertaining to local installations of HHpred/HHblits.

Cite Us

If you use our Toolkit for your research, please cite us. It helps us keep this service running for you.

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core.
Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V. J Mol Biol. 2017 Dec 16. S0022-2836(17)30587-9.
Recent Updates

March 29, 2018

HHpred: profile HMM database of Acinetobacter baumannii is online.

March 7, 2018

HHpred: a new version of the SCOPe database, version 2.07, is now online.

March 4, 2018

HHpred: a new version of the ECOD database, version 20180219 (develop204), is now online.

December 24, 2017

Our paper on the new Toolkit is out: A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V. J Mol Biol. 2017 Dec 16.

December 6, 2017

HHpred: the PDB_mmCIF70 DB is now built using Uniclust30 instead of Uniprot20. Additionally, we now also offer PDB_mmCIF30, containing fewer representatives.

December 5, 2017

HHpred: profile HMM DBs of six archaeal proteomes (Archaeoglobus fulgidus, Halobacterium jilantaiense, Methanocaldococcus jannaschii, Methanothermus fervidus, Pyrococcus horikoshii, and Sulfolobus solfataricus) are online.

November 13, 2017

In addition to nr50, we now also offer nr30 for PSI-BLAST, HMMER, and PatternSearch.

October 31, 2017

HHpred: the Uniclust30 DB is now available for query A3M generation.

September 29, 2017

HHblits: a new version of the Uniclust30 DB is online.

September 24, 2017

HHpred: profile HMM DBs of Fischerella muscicola, Frankia alni, Streptomyces scabiei, and Thermus aquaticus are online.

September 19, 2017

HHpred: profile HMM DBs of Aquifex aeolicus, Deinococcus radiodurans, Dictyostelium discoideum, Schizosaccharomyces pombe, and Thermus thermophilus are online.

September 9, 2017

HHpred: profile HMMs of the ECOD database (Grishin Lab) are online.

August 31, 2017

HHpred: HMM database of Giardia lamblia is online.

August 28, 2017

HHpred: HMM database of Physcomitrella patens is online.

August 23, 2017

HHpred: HMM databases of Brachypodium distachyon and Tetrahymena thermophila are online.

July 21, 2017

Our Quick2D tool for the annotation of protein secondary structural features is back.

July 18, 2017

HMM databases of Caenorhabitis elegans and Drosophila melanogaster are online.

July 10, 2017

HMM databases of the COG, KOG, SMART, and NCBI CD databases are online now.

July 4, 2017

Profile HMM databases of the human proteome and Chaetomium thermophilum are online.

June 20, 2017

Profile HMM database of Arabidopsis thaliana is online.

June 10, 2017

Profile HMM databases of many bacterial proteomes are online.

May 27, 2017

Profile HMM databases of Mycobacterium tuberculosis is now available for HHpred.

May 19, 2017

Release Notes: Welcome to the new version of the MPI Bioinformatics Toolkit

Dear Toolkit Users,

welcome to the new version of the MPI Bioinformatics Toolkit hosted at the Department of Protein Evolution, Max Planck Institute for Developmental Biology, Germany. The first version of the Toolkit was released in 2005 and has serviced over 2.5 million external queries to date. We had to rework the Toolkit entirely because of mounting software incompatibility with our computing infrastructure and also took this opportunity to improve some features and prune a few of the outdated and less-widely used tools. To allow an easy transition to the new Toolkit, we have retained the basic structure and UI features of the earlier version, and have added additional features, some of which are listed below, to enhance user experience.

New tools

  • PhyML is offered instead of PHYLIP-NEIGHBOR for phylogenetic inference.
  • MMseq2s is offered instead of BLASTClust for clustering of up to 20,000 sequences.

New features/changes

  • HHpred allows comparison of two sequences or MSAs, replacing HHalign.
  • CLANS allows clustering of up to 10,000 sequences.
  • BLAST+ and PSI-BLAST+ are offered as a single tool.
  • Caching of results for quick retrieval of pre-computed jobs.
  • Search box on the index page for quick access to tools and jobs.
  • Job manager in addition to joblist for easy management of jobs.
  • E-mail notifications are only available to logged-in users.
  • Comprehensive client-side input validation.
  • Significantly enhanced performance, owing to upgraded computational infrastructure.

Coming soon
We are going to bring back FRpred, HHomp, Quick2D, daTAA, and REPPER within the next few weeks. Additionally, we are going to offer many more proteome databases for HHpred over the next months and are also working on making the help pages more comprehensive.

The new Toolkit is still under active development and we invite you to send us your feature requests and bug reports ( ).

If you find our Toolkit useful for your research, please cite us (Alva et al., 2016) ; it helps us keep this service running for you.

Best wishes,
Your Toolkit Team