Welcome to radar radar is free software. Please see the file COPYING for details. 1. Requirements RADAR is written in ANSI C and should compile on most platforms. The executable is called 'radar'. There is a python installation, which requires cython (http://cython.org) for compilation and will install 'radar.py' Both radar and radar.py require the lfasta program from W.R. Pearson's fasta package. To install this, execute the following commands: mkdir fasta2 cd fasta2 wget http://faculty.virginia.edu/wrpearson/fasta/fasta2/fasta2.shar.Z gunzip fasta2.shar.Z sh fasta2.shar make lfasta Copy the newly built 'lfasta' executable into a directory on your path. 2. Installation: 2.1 retrieve the latest from http://sourceforge.net/projects/repeatradar 2.2 extract source files tar -xvzf radar-x.x.x.tgz cd radar-x.x.x.tgz 2.3 configure the package ./configure 2.4 radar.py: installation python interface to radar (recommended) python setup.py install This will install radar.py in your path. Please make sure you have the appropriate permissions. 2.5 radar: classic installation of C executable make; make install 3. Usage of radar.py Please execute radar.py -h or radar.py --help for usage instructions. Radar.py accepts FASTA formatted input and can process multiple sequences and files. The simplest use case is radar.py < ./example/finc.fasta 4. Usage of radar (classic C executable) Before you find out yourself, the user interface to radar is pretty basic and not very comfortable and fault-tolerant, hence the newer radar.py. Unless you want to supply a multiple alignment to radar use of radar.py is much more comfortable. The basic usage is the following: radar -P c -Q c -R c [-S c] [-V n] where the parameters are -P filename of the multiple alignment -Q filename of lfasta-output -R filename of the sequence -S filename of sequence lfasta-file[optional] -V level of verbosity. 0 is lowest, 4 is highest. The multiple alignment file should contain the rows separated by newlines. The sequence file should just contain the sequence. The lfasta-files contain the output of the lfasta program. See the directory ./example for templates for these files. You can run the example by typing ./src/radar -P example/finc.ma -Q example/finc.lfasta1 -R example/finc.seq -S example/finc.lfasta2 after compilation. If you do not have a multiple alignment, you can also run radar in single sequence mode. Simply provide the sequence itself as the multiple alignment by providing the sequence twice: ./src/radar -P example/finc.seq -Q example/finc.lfasta1 -R example/finc.seq -S example/finc.lfasta2