NCBI C Toolkit Changes Since Version 2.2.9
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1. BlastPGP
        - added code to spread out gap costs when extracting 
                data from the sequence alignment to build PSSM
        - changed handling of all-zero columns of residue frequencies 
                to use the underlying scoring matrix frequency ratios 
                rather than scoring matrix's scores
        - disallowed an ungapped search if more than one iteration 
                is specified
        - added input/output of residue frequencies as scoremat objects

2. Score-mat objects
        - changed ASN.1 specification for Score-Matrix to use floating 
                point instead of fixed point for residue frequencies
                and weights
        - added a new 'formatrpsdb' application; given a collection of
                Score-mat ASN.1 files, this application creates a database
                suitable for use with RPSBLAST

3. General changes:
        - consolidated formatting code
        - removed fmerge.c
        - small fixes to sum statistics code
        - better error handling
        - fixed masking of translated queries
        - fixed several readdb threading bugs