GULL is an unsupervised tool for measuring relative similarity between non-assembled genomic sequences.
Cmake is needed for installation (http://www.cmake.org/). You can download it directly from http://www.cmake.org/cmake/resources/software.html or use an appropriate packet manager. In the following instructions we show the procedure to install GULL:
git clone https://github.com/pratas/GULL.git cd GULL/src/ cmake . make cp GULL-map ../../ cp GULL-visual ../../ cd ../../
This will create two binary files:
GULL-map
to measure the similarity between sequences and
GULL-visual
to visualise the similarity in a heatmap scheme.
To see the possible options type
./GULL-map ./GULL-visual
or
./GULL-map -h ./GULL-visual -h
These will print the parameters that are needed to run both tools.
For GULL-map:
Usage: GULL-map [OPTION]... [FILE1]:[FILE2]:...
A tool for measuring relative similarity between
non-assembled genomic sequences without supervision.
Non-mandatory arguments:
-h give this help,
-V display version number,
-v verbose mode (more information),
-s how compression levels,
-l <level> compression level [1;30],
-n <nThreads> number of threads,
-x <FILE> similarity matrix filename,
-o <FILE> labels filename,
Mandatory arguments:
<FILE>:<FILE>:<...> input files (last arguments).
Use ":" for file splitting.
Report bugs to <{pratas,raquelsilva,ap,pjf}@ua.pt>.
For GULL-visual:
Usage: GULL-visual [OPTION]... [FILE]
A visual heatmap builder for any similarity matrix.
Non-mandatory arguments:
-h give this help,
-V display version number,
-v verbose mode (more information),
-w square width (for each value),
-a square inter-space (between each value),
-s index color start,
-r index color rotations,
-u color hue,
-g color gamma,
-l <FILE> labels filename,
-x <FILE> heatmap filename,
Mandatory arguments:
<FILE> input matrix file (last argument).
Report bugs to <{pratas,raquelsilva,ap,pjf}@ua.pt>.
The following map shows and example while measuring similarity between human (HS), chimpanzee (PT) and gorilla (GG) chromosome sequences, including unplaced (UP), unlocalized (UL) and mitocondrial (MT) sequences.
On using this software/method please cite:
Paper submitted.
For any issue let us know at issues link.
GPL v3.
For more information:
http://www.gnu.org/licenses/gpl-3.0.html