freecontact
fast protein contact predictor
Command lineScience
Not tested on a device yet. What that means
Commands in the package
freecontact
About freecontact
From Debian's package description
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.
This package contains the command line tool freecontact(1).
From Debian's description of the freecontact package, under that package's license.
Dependencies
Depends on
libboost-program-options1.83.0libc6libfreecontact0t64libgcc-s1libstdc++6libxerces-c3.2t64perl
Related apps
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PyQSOContact Logging Tool
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the freecontact package, under that package's license.
- Description: Debian's description of the freecontact package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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