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TraceTuner 3.0.6 beta Release Notes                         June 30, 2009
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Introduction
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These notes describe beta release of TraceTuner version 3.0.6, which is
identical to previous 3.0.x beta releases, except for bug fixes. This code    
compiles on Linux platform and MS DOS using GNU C compiler. In addition to 
executable ttuner, it supports seven new executables:  train, trainphd, lut, 
checkbc, checkbcphd, checkqv and checkqvphd. It also includes algorithmic and 
interface improvements for ttuner over the previous releases 2.0.x and allows 
an updated set of built-in calibrations of quality values.

The major new features in 3.0.x release:

    o   Availability of the source code for calibration of quality values. 
        Thus, the use of this code will allow automatic generation of 
        customized calibrations (a.k.a. lookup tables) from user-supplied 
        Sanger sequencing datasets.

    o   Availability of tools for checking the accuracy of base calls and 
        quality values produced by TraceTuner, as well as by any other
        base calling program which supports output of PHD file.

    o   Support for detection of heterozygous indels in diploid or mixed
        DNA samples, as well as for deconvolving "mixed" electropherograms 
        resulting from the presence of heterozygous indels into a couple
        of "pure" electropherograms representing the long and short haplotypes.

    o   Updated procedure for calling heterozygous SNPs/mixed bases and
        evaluaing their quality values in diploid and/or mixed DNA samples.

    o   All the executables can be built not only on Linux/Unix platform,
        but also in MS DOS.
    
    o   Built-in generic calibrations are available for ABI 3730 and MegaBACE 
        sequencing platforms.

    o   No node-locked license will be required for running this code.

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Modification History
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2.0.9:				

    o   TT: Updated to use node-locked license.

    o   TT: Added support for .poly file output.

    o   TT: Fixed a problem that the base calling was dependent on the color 
	ordering.

    o   TT: Fixed a problem that was giving "Error calling Btk_process_peaks" 
	error message.

    o   TT: Fixed out-of-order base calling.

    o   TT: Fixed a problem that could sometimes result in assigning zero 
	height to a peak when identifying peak boundaries.

    o   TT: Improved the pure base-calling algorithm, which takes more care 
	of the spacing of called bases.

    o   TT: Improved the algorithm for finding the "best" candidate base 
	regarded as "inserted" base.

    o   TT: Optimized some parameters for better performance.

    o   Launcher: Added *.abd filter (for Cimarron basecaller) in the file
	browser.

    o   Launcher: Changed the default value for minimum peak height ratio 
        from 0.15 to 0.1.

    o   Launcher: Updated online help.


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Known Bugs/Issues/Limitations with this release
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    o   The command-line interface does not support processing compressed
	chromatogram files on non-UNIX platforms.

    o	The the Viewer Java Interface does not support the reading of 
        compressed or .gz chromatogram files.

    o	In the Viewer Java Interface, "Print Global View of All Files" option
	in the "File" menu requires printing destination to be set as the
	system-default printer.  Problems may occur if the printing 
	destination is set to non-system-default printers or files, when 
	utilizing this print option.


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Copyright (c) 1999-2003, Paracel, Inc.  All rights reserved.
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