Difference between revisions of "FreeContact"

From Rost Lab Open
(Initial version)
 
(Debian)
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can be used to generate the alignments, for example.
 
can be used to generate the alignments, for example.
   
=== FreeContact Sources ===
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== FreeContact in Debian and Derivatives ==
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FreeContact and the Perl and Python modules are available in Debian, and are or will soon be available in derivative operating systems such as Ubuntu, Bio-Linux and CloudBioLinux.
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=== Debian ===
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* FreeContact: http://packages.debian.org/freecontact
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* FreeContact for Perl: http://packages.debian.org/libfreecontact-perl
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* FreeContact for Python: http://packages.debian.org/python-freecontact
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== FreeContact Sources ==
   
 
Open source code for FreeContact and its Perl and Python modules is available at ftp://rostlab.org/free/.
 
Open source code for FreeContact and its Perl and Python modules is available at ftp://rostlab.org/free/.

Revision as of 11:43, 3 October 2013

Welcome to the FreeContact Home Page

FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

FreeContact in Debian and Derivatives

FreeContact and the Perl and Python modules are available in Debian, and are or will soon be available in derivative operating systems such as Ubuntu, Bio-Linux and CloudBioLinux.

Debian

FreeContact Sources

Open source code for FreeContact and its Perl and Python modules is available at ftp://rostlab.org/free/.