 Spa : A probabilistic algorithm for Spliced Alignment
  
 Platform :
	gcc 3.2.1 or later
	libc.so.1 or later
	libstdc++.so.5.0.1 or later

 To generate the Spa excutable  program :
	- decompress the tarball : tar -xzvf spa.tar.gz
	- cd Spa
	- make
	- make spa-parse

 To run the Spa program, make sure that the gfServer is running and run :
	- spa <host> <port> <spa_top_parameters filename> <spa_parameters filename> <nibDir> <infile.fa> <outfile.mach>
	  <host> is the server name where gfServer is running
	  <port> is the port number where gfServer can receive requests
	  <spa_top_parameters file> user modifiable parameter file 
	  <spa_parameters file> scoring scheme parameters
	  <nibDir> path where nib files are
	  <infile.fa> input fasta file
	  <outfile.match> output file
	
 To convert in sim4-like format run :
	- spa-parse outputfile.match outputfile.hum
 
Enjoy Spa!

