
	SIBIS: Bayesian Inconsistency in Sequences
                        (version 1.0, Feb 2014)

Please send bug reports, comments etc. to :-
        thompson@unistra.fr

******************************************************************************

SIBIS (SIBIS is Bayesian Inconsistency in Sequences) is written in ANSI-C which can be run on any machine 
with an ANSI-C compiler. 

The program cluspack, written by N. Wicker (a program for clustering sequences in a multiple alignment, 
previously called secator) is required. The source files for cluspack are provided in the 
cluspack.tar file.

One tcsh script is provided to run the programs in the correct order:

sibis.tcsh


Installation:
------------

To untar the archive, type:

tar -xvf sibis_src.tar

This should create a directory called SIBIS1.0. To compile the C programs, type:

cd SIBIS1.0
make
tar -xvf cluspack.tar
cd cluspack_src
make

Copy the C programs and sibis.tcsh to a directory in your PATH. Edit the sibis.tcsh file
to point to this directory.

Usage:
-----

sibis.tcsh input_file output_xml_file output_log_file

	where input_file is the initial alignment file in MSF format or FASTA format
	     output_xml_file is the alignment file created by SIBIS in XML format
	     output_log_file is the formatted log file created by SIBIS

An example alignment is provided in the SIBIS archive. The command line used to produce the output
files is shown here:

sibis.tcsh test.fasta test.xml test.log

The output of SIBIS consists of 2 files. The first contains the multiple alignment, with
inconsistent segments annotated. The second file is a text file, giving more details of the
SIBIS calculations. 

The inconsistent segments are annotated as:
SEQ_ERRORN1	N-terminal extension
SEQ_ERRORN2	N-terminal deletion
SEQ_ERRORC1	C-terminal extension
SEQ_ERRORC2	C-terminal deletion
SEQ_ERROR1	insertion
SEQ_ERROR2	deletion
SEQ_ERROR3	inconsistent segment
