LEON-BIS


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Installation:
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The program cluspack is required. The source files for cluspack are provided in the cluspack_src file.
To compile the C programs, type:
	cd cluspack_src
	make

chain_blocks from LEON is required. The source files for Leon are provided in the leon_src file.
To compile the C programs, type:
	cd leon_src
	make


A jar file called leon-bis.jar is provided.


A tcsh script is provided to run all the programs :
	leon-bis.tcsh

You may need to edit the leon-bis.tcsh file to point to the cluspack and chain_blocks directories.



Usage:
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leon-bis.tcsh aligment_name query_sequence output_xml_file output_log_file

	where:
	alignment is the input alignment file in MSF format or FASTA format
	query_sequence is the name of the query sequence
	output_xml_file is the name of the output alignment file in XML format
	output_log_file is the name of the output text formatted file


To convert the XML format output file to MSF or FASTA

leon_src/convseq xml_file output_file gcg

or

leon_src/convseq xml_file output_file fasta
