1. Download foursaleDownload 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
- Download and install JRE (Java Runtime Environment) >= 1.5 from the Java download page.
- Download and install ClustalW2 2.1 from the Clustal download page
3. Run foursale on command linejava -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 If clustalw2 is in your PATH environment variable this option is obsolete.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: email@example.com