Usage


1. Download foursale

Download foursale command line from the Download section and unzip the content. You will find a folder called "examples", and a file called "foursale.jar" inside the zip. The "examples" folder contains a file (Cnidaria.xfasta) in the typical xfasta format.

2. Install required dependencies

3. Run foursale on command line

java -jar foursale.jar -in C:/Downloads/examples/Cnidaria.xfasta -out C:/Downloads/examples/Cnidaria_AL.xfasta

A full description of all arguments is available by: java -jar foursale.jar -h

					 
usage:
                java -jar foursale.jar [-clustalw2 ] [-gapextend ] [-gapopen ] [-h]
                [-help] [-in ] [-matrix ] [-out ] [-quiet] [-version]

Foursale, the command line version of 4SALE, allows you to perform alignments on sequence and
secondary structure simultaneously. Therefore, sequences and structures are transformed
into a 12-letter code alphabet (see translation table below). Using a specific 12-letter
code scoring matrix, the alignment is performed by using ClustalW2. Afterwards, the 12-letter
code alignment is re-transformed to aligned sequences and structures.
--
Sequences :     AAA CCC GGG TTT UUU NNN
Structures:     (). (). (). (). (). ().
12-letter code: ARN DCQ EGH ILK ILK YZX
--
If you use this software, please cite: []
For updates, please see [http:4sale.bioapps.biozentrum.uni-wuerzburg.de]
.
     -clustalw2      Fully qualified path including a filename to clustalw2.exe or clustalw2
                          binary. If clustalw2 is in your PATH environment variable this option
                          is obsolete.
     -gapextend      Gap-extend costs for the alignment (default: 0).
     -gapopen        Gap-open costs for the alignment (default: 0).
     -h              Print usage information about foursale.
     -help           Print usage information about foursale.
     -in             Fully qualified path including a sequence filename in XFASTA format.
     -matrix         Scorematrix for the alignment (12-letter code).
     -out            Fully qualified path including a sequence filename for the aligned XFASTA
                          output.
     -quiet          Perform all operations in silent mode and suppress any output to stdout.
     -version        Print foursale version information.

(c) University of Wuerzburg 2014
For further comments please email Dr. Matthias Wolf at: matthias.wolf@biozentrum.uni-wuerzburg.de