    Release History
    ---------------

    Notes for the 2.2.10 release
    ----------------------------

    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:
            - megablast now performs ungapped extensions in order to prevent suboptimal alignments
            - 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
            - improved protein neighbor generation
            - hsp sorting/inclusion fixes from Mike Gertz
            - many changes in HSP linking by Mike Gertz
            - several fixes for translated RPS blast

    4. New engine:
            - We have been rewriting and refactoring the BLAST engine in order to make it more modular and extensible. C and C++ APIs will be available. bl2seq and megablast are currently compiled with support for the new engine; it can be enabled with the -V F option.

    5. General interest

    NCBI now provides anoncvs access to toolkit sources.

    A cvsweb source browser and doxygen documentation are also available.

    Notes for the 2.2.9 release (5 May 2004)
    ----------------------------------------
    Bugs fixed:
     * A serious error in copymat which caused incorrect databases to be
       produced has been fixed.
     * A number of problems with query concatenation in blastall have been fixed.
     * XML output was brought in sync with text output by adding masking of the
       filtered locations in query sequences.

    Changes:
     * formatdb can no longer produce old-style BLAST databases.

    Performance improvements:
     * For translating searches of large sequences, only the needed pieces of
       the sequence are translated during the traceback.
     * The performance of reading binary gilists has been improved.
     * formatdb now produces 1 gigabyte volumes by default on 32-bit platforms
       in order to prevent mmap() failures.
     * When possible, use approximate sequence lengths for search space calculation.
     * DUST filtering was made more aggressive.

    Statistical improvements:
     * Unified handling of gapped Karlin blocks between protein and nucleotide
       cases.
     * Adjustments to the lengths of query and database sequences have been
       improved.
     * Composition-based statistics routines were refactored.

    Ongoing software engineering improvements:
     * Fixed memory leaks.
     * Fixed uninitialized variables.
     * Fixed null pointer handling.
     * Dead code and variables were eliminated.
     * Many compiler/type warnings fixed.

    Notes for the 2.2.8 release:

    * Correction to tblastx alignment computation

    Notes for 2.2.7 release (2/2/04):

    * Standalone BLAST is now available for amd64-linux.

    * formatdb now restricts volume sizes to 1G on 32-bit platforms
      for performance reasons.

    * The -A option has been removed from formatdb, that is, all databases
      will be created with ASN.1 deflines.

    * tblastn query concatenation now works correctly on 64-bit platforms.

    * The wwwblast source code has been merged into the C toolkit tree and
      is no longer distributed with the binaries.

    Notes for 2.2.6 release (4/9/03):

    Enhancements:

    1.) A -B option now exists for blastall that specifies the concatenation of queries
    for blastn and tblastn.  This option is still experimental and subject to change.
    It is not supported with XML, ASN.1, or tabular output.

    2.) Text and binary SeqAligns can now be produced in place of the standard BLAST report by
    using (respectively) "-m 10" or "-m 11".

    Bug fixes:

    1.) A problem with an integer "rollover" in formatdb has been fixed.  This happened when the
    volume size was selected with the -v option and the specified number of bases became negative and
    the option was ignored.

    2.) A problem in the statistics of the BLAST output footer was fixed.  This was a double-counting of
    the number of extensions performed.

    3.) A problem that caused the target and query sequences to be reversed in tblastx XML output has been fixed.

    4.) A memory corruption problem in the formatting of the tabular output has been fixed.

    5.) An unstable sorting problem in the results for tblastx searches has been fixed.

    6.) A spurious error message about a file called "taxdb.bti" has been suppressed.

    7.) A problem with the number of hits returned in XML mode being double what they should be has been fixed.

    8.) The fastacmd return values have been corrected, it is 0 on success and 1 for an error.

    Notes for 2.2.5 release (11/15/02):

    Enhancements:

    1.) Fastacmd now prints the length of the longest sequence
    when used with the -I option.

    2.) It is now possible to specify a range restriction on the query for
    an rpsblast search, use the -L option.

    Bug fixes:

    1.) A problem that caused bl2seq to not show the ID of the query has
    been fixed.

    2.) A problem that caused formatdb to not properly work on the nr protein FASTA file
    has been fixed.

    3.) A problem that caused blastall or blastpgp to print too many alignments when
    used with XML mode has been fixed.

    4.) The -P option was accidentally deleted from the blast binaries in the 2.2.4 release
    and has been restored.  The -P option can be used to specify whether one or
    two hits should be found before an extension, the default is two hits.

    Notes for 2.2.4 release (08/26/02):

    Enhancements:

    1.) Discontiguous word matching is now available for megablast.
    See http://www.ncbi.nlm.nih.gov/blast/discontiguous.html for details.

    2.) An out-of-frame gapping option (meaning that one or two bases can be
    inserted or deleted from an alignment) is now available in blastall for
    blastx and tblastn.  NOTE that the expect values have been calculated
    assuming in-frame gapping (three bases inserted/deleted) and should only
    be used for guidance.

    3.) Fastacmd can now dump out partial sequences (using the -L option)
    and print taxonomic information for a sequence.

    Bug fixes:

    1.) A problem that caused blastall to core-dump when the -U option
    (mask the sequence that is lower-case in input file) has been fixed.

    2.) A problem that caused bl2seq to not work properly for protein-protein
    searches with BLOSUM62 (on some platforms) has been fixed.

    3.) A problem that caused seedtop to core dump if there were a lot
    of hits has been fixed.

    4.) Using -n with blastall (megablast mode) now returns the same results
    as default megablast.

    5.) XML output for megablast has been fixed.

    6.) A problem with translating rpsblast that caused it to crash on OSF/1
    and report incorrect values on other platforms has been fixed.

    7.) A memory leak in formatdb was fixed.

    8.) A problem that caused blastpgp to core-dump when running in PHI-BLAST mode
    (if many hits were found) was fixed.  Memory leaks were also fixed.

    9.) the double closing of a file that caused phi-blast to crash occassionally
    under LINUX has been fixed.

    Notes for 2.2.3 release (04/24/02):

    Enhancements:

    1.) Version 4 of the BLAST databases is now the default for formatdb.
    This can be overridden for older binaries by use of "-A F" on the
    command-line.

    Bug fixes:

    1.) A problem has been fixed that caused tblastn searches to miss some protein matches,
    if the database sequence was longer than 15 million bases.

    2.) Selenocysteine residues (U) in the query are now replaced by X's as these
    are not supported in the currently available matrices (e.g., BLOSUM62), so that
    their presence occasionally caused data corruption.

    3.) A problem with combining the "-m 7" and "-n T" options in blastall has
    been fixed.

    4.) XML output had a <Hit_def> field that could (incorrectly) have an empty value,
    this has been fixed.

    5.) A problem with reading databases with more than one volume and an oidlist has
    been fixed.

    6.) A problem with ungapped XML output that caused all HSP's to be number zero
    has been resolved, they are now numbered with one-offset.

    7.) A bug that prevented use of some matrices for ungapped searches has
    been fixed.

    8.) Effective query and database lengths were calculated incorrectly for
    rpsblast, leading to a minor change in expect values in some cases.  This
    has been corrected.

    9.) A for loop that could overrun the end of a buffer during formatting was
    fixed.  Many thanks to Haruna Cofer of SGI for pointing this.

    10.) The effective database length command-line argument (-z) has been fixed
    for blastall and megablast.  The parser was reading digits only until
    there were no non-digits (e.g., 1.6e8 was interpreted as "1"), leading
    to wildly incorrect effective database lengths.  This has been fixed so
    that 160000000 and 1.6e8 are interpeted the same way.

    Notes for 2.2.2 release:

    Enhancements:

    1.) Version 4 of the BLAST databases is now fully supported.  This version
    has some enhancements described in README.formatdb and fixes some problems
    described below.  Use the "-A" option on formatdb to produce the new database
    version.  The BLAST binaries for release 2.2.2 are entirely compatiable with
    both the current and the new version of the BLAST databases.  Old BLAST binaries
    are not necessarily compatiable with the new database format.

    2.) Fastacmd will dump out an entire BLAST database in FASTA format if the
    new -D option is used.

    3.) Fastacmd will separate definition lines from different GI's that have
    been merged together in nr (as they all have the same sequence) by control-A's.
    if the new -c option is used.

    Bug fixes:

    1.) A problem has been fixed that caused tblastn searches to miss some protein matches,
    if the database sequence was longer than 15 million bases.

    2.) The old (current) version of the BLAST databases has a "rollover" problem if
    the total number of bases in a single volume is greater than 4294967295.  The new
    database verison (#4) allows eight bytes for this.

    3.) The old (current) version of the BLAST database format does not handle ambiguity
    characters in a nucleotide database sequence if it is over 16 million characters long.
    The new version of the the BLAST database does.

    4.) A performance problem that caused a mutexes to be acquired too often for
    multi-threaded runs with four or more CPU's has been fixed.  Thanks to Haruna
    Cofer of SGI for help in finding the cause.

    5.) A problem that caused ungapped blastp/blastx/tblastn/tblastx to crash on
    certain matrices (e.g., pam10) has been fixed.

    6.) Some blastpgp problems with using the -B (for reading a master-slave alignment) and
    reading checkpoint files (-C) have been resolved.

    Notes for 2.2.1 release:

    Enhancements:

    1.) BLAST and PSI-BLAST improvements as described in
    Schaffer et al., Nucleic Acids Research 2001 Jul 15;29(14):2994-3005.
    These include improvements the use of composition-based statistics
    and improvements to the edge-correction effects.  Composition-based
    statistics were initially implemented in release 2.1.1, but the
    implementation is improved in release 2.2.1.

    2.) Formatdb automatically produces database volumes for input
    consisting of more than 4 billion letters.

    3.) Formatdb can produce an alias file for a given database and GI list
    as well as convert a GI list to the more efficient binary format.  See
    details in README.formatdb.

    4.) RPSBLAST now works properly with 'scaled' databases.  The scaling factor must
    be set when executing the program 'makemat' (which takes PSI-BLAST checkpoints
    as input).  Scaling-up the matrix improves the precision of the (integer) calculations.

    5.) Tabular output has now been added to blastpgp and rpsblast, use the "-m 8" option.

    6.) Blastpgp will now process multiple queries.

    Bug fixes:

    1.) A problem with the -K option (for culling) that caused BLAST to crash has been fixed.

    2.) A problem with the "gnl" identifier and multi-volume databases has been fixed.

    3.) A problem that caused BLASTN to very rarely find suboptimal alignments has been fixed.

    4.) A problem that could cause makemat to crash has been fixed.

    4.) Some multi-threading problem pointed out by Henry Gabb of KAI were fixed.

    5.) Some PC-lint errors and warnings pointed out by Russ Williams of United Devices
    were fixed.

    Notes for 2.1.3 release:

    Enhancements:

    1.) Addition of PSI-TBLASTN ability to blastall, see description in
    README.bls.

    2.) Database sequences over 5 million bases in length are now broken
    into chunks to keep memory usage reasonable.

    3.) Blastall now allows one to enter a location if it is desired
    to search a subsequence of the query.

    4.) Formatdb can produce a new BLAST database format using the -A option.
    The BLAST programs can read this format as well as the current format (the
    program automatically identifies which version it should work with).  This
    new format stores the sequence definition lines in a structured manner
    (as ASN.1), this will allow future versions of BLAST to better present
    taxonomic information as well as information about other resources (e.g.,
    UniGene, LocusLink) for a database sequence.

    5.) Blastall can now produce tab-delimited, use "-m 8" to specify this.

    6.) Improved Karlin-Altschul parameters are now being used, they were
    calculated using the "island" method

    7.) A "gapped" check was added to BLASTN to ensure that if a hit is low-scoring
    after an ungapped extension, but high-scoring after a gapped extension, it will
    not be missed.

    8.) The formatdb error messages have been improved for the case of illegal
    characters in the sequence.

    9.) The number of HSP's saved in an ungapped search has been increased to 400 from 200.

    Bug fixes:

    1.) A problem with XML output was fixed.

    2.) A problem with the seg filtering under LINUX was
    fixed (many thanks to Eric Cabot at GCG for pointing this out).

    3.) A problem with format of BLAST reports if the "-o" flag
    was not used when the database was produced was fixed
    (thanks again to Eric Cabot).

    4.) A problem with reading the BLAST database caused by a 4-byte signed integer
    than should have been unsigned was fixed (thanks to Haruna Cofer at SGI
    for pointing this out).

    5.) A problem with copymat under NT and IRIX was fixed.

    Notes for 2.1.2 release:

    Enhancements:

    1.) Release of rpsblast.  Rpsblast performs a search against a database
    of profiles.  See README.rps for full details.

    2.) Release of blastclust.  BLASTCLUST automatically and systematically clusters protein sequences
    based on pairwise matches found using the BLAST algorithm.   See README.bcl for
    full details.

    3.) Release of megablast.  Megablast uses the greeedy algorithm of Webb Miller et al.
    for nucleotide sequence alignment search and concatenates many queries to save
    time spent scanning the database.   See README.mbl for full details.

    4.) XML output can now be produced.  Use the '-m 7' option for this.
    The XML output is still experimental.

    5.) the default behavior the culling (-K) option has been changed.  Previously
    this option was set to 100, meaning that if more than 100 HSP's had a
    hit to a region lower scoring ones would be dropped.  The option is now
    zero, which turns off this behavior.  In a few cases this change will
    result in more database sequences being reported.  The previous behavior can
    be recovered by using '-K 100' on the command-line.

    Bug fixes:

    1.) A bug that caused only the last SeqAnnot to be written (if the -O option
    was used) when multiple sequences were searched has been fixed.  All
    SeqAnnots are printed out.

    2.) A bug that caused the search space (set on the command line with the -Y option)
    to be ignored for some blastx and tblastn calculations has been fixed.

    3.) A failure to close a file if a gilst was used (using the -l option) was
    fixed.  Many thanks to David Mathog at CalTech for spotting this problem
    and suggesting a fix.

    4.) A bug that caused all the database names listed in an alias file to be
    printed, rather than the "TITLE" field has been fixed.

    Notes for 2.1.1:

    Enhancements:

    1.) Addition of compostion-based statistics:

    BLAST and PSI-BLAST now permit calculated E-values to take into account the amino acid composition of the individual database sequences involved in reported
    alignments. This improves E-value accuracy, thereby reducing the number of false positive results.

    The improved statistics are achieved with a scaling procedure [1,2] which in effect employs a slightly different scoring system for each database sequence. As a result,
    raw BLAST alignment scores in general will not correspond precisely to those implied by any standard substitution matrix. Furthermore, identical alignments can receive
    different scores, based upon the compositions of the sequences they involve. The improved statistics are now used by default for all rounds of searching on the
    PSI-BLAST page, but not on the BLAST page. Therefore, if one uses default settings, the results of the first round of searching will be different on the BLAST and
    PSI-BLAST pages.

    In addition adjustments have been made to two PSI-BLAST parameters: the pseudocount constant default has been changed from 10 to 7, and the E-value threshold for
    including matches in the PSI-BLAST model has been changed from 0.001 to 0.002.

    1. Altschul, S.F. et al. (1997) Nucl. Acids Res. 25:3389-3402.
    2. Schäffer, A.A. et al. (1999) Bioinformatics 15:1000-1011.

    Notes for 2.0.14 release:

    Bug fixes:

    1.) extra line returns between sequences in the a FASTA file
    causes formatdb to produce corrupted databases.

    2.) ";" at the beginning of a line was not being treated as a comment.

    3.) a problem with the formatter causes blast to core-dump if
    the FASTA definition line only contains an identifier and
    no description.

    4.) a problem in the ungapped extension for protein sequences
    causes a rare problem.

    5.) the '-U' option that causes lower-case sequence to be masked
    does not work correctly for blastx.

    Notes for 2.0.13 release:

    Enhancements:

    1.) The output format for pairwise alignments was changed to
    put each new gi (if the sequence has redundant gi's) on a
    new line.  If HTML output is specified then each gi is hyperlinked.

    Bug fixes:

    1.) An NCBI toolkit problem parsing the new RefSeq format in FASTA files
    (two bars instead of three) was fixed.  This fix applies to all
    BLAST binaries (formatdb, blastall, blastpgp, etc.).

    2.) A problem that caused BLAST version 2.0.12 under NT to freeze in
    multithreaded mode has been fixed.

    Notes for 2.0.12 release:

    Enhancements:

    1.) Bl2seq can now perform nucleotide-protein (blastx style) comparisons.
    This necessitated changing the '-p' option from a Boolean to a
    string.  Valid arguments are "blastn", "blastp", or "blastx".

    Bug fixes:

    1.) A problem in the NCBI threads library that caused BLAST to sometimes
    stick was corrected.  Many thanks to Haruna Cofer and colleauges at SGI
    for providing a fix.

    2.) A problem that caused BLAST to core-dump (especially on long queries)
    has been fixed.  Many thanks to Gary Williams for providing examples.

    3.) A problem that prevented the search of multiple multivolume databases
    has been fixed.

    Notes for 2.0.11 release:

    Enhancements:

    1.) Optimizations were contributed by Chris Joerg of COMPAQ.  These changes
    reduce the number of cache misses, unroll loops, and make some instructions
    unnecessary.  These improvements can speed up BLAST for long sequences
    several-fold.

    2.) A database is now only memory-mapped while being searched.  If multiple databases
    are searched and the total exceeds the allowed memory-map limit this allows
    all databases to be searched as memory-mapped files.  If a database cannot
    be memory-mapped it is read as an ordinary file, rather than causing an error.

    Bug fixes:

    1.) Formatdb was fixed to correct a problem with FASTA string identifiers under NT.

    2.) Blastpgp was fixed to prevent a core-dump under LINUX

    3.) BLASTN was found to miss some hits near the expect value cutoff.  This has been
    corrected.

    Notes for 2.0.10 release:

    Enhancements:

    1.) Bl2seq, a utility to compare two sequences using the blastn or blastp approach,
    is included in the archive.  See the full description in the README.bls for details.

    2.) A 'sparse' option ('-s') has been added to formatdb.  This option limits the indices
    for the string identifiers (used by formatdb) to accessions (i.e., no locus names).
    This is especially useful for sequences sets like the EST's where the accession and locus
    names are identical.  Formatdb runs faster and produces smaller temporary files if this
    option is used.  It is strongly recommended for EST's, STS's, GSS's, and HTGS's.

    3.) A volume option ('-v') has been added to formatdb.  This option breaks up large
    FASTA files into 'volumes' (each with a maximum size of 2 billion letters).
    As part of the creation of a volume formatdb writes a new type of BLAST database file,
    called an alias file, with the extension 'nal' or 'pal', is written.  This option
    should be used if one wishes to formatdb large databases (e.g., over 2 billion
    base pairs).

    4.) It is is now possible to jump start the command line version of PSI-BLAST (blastpgp)
    from a multiple alignment that includes the query sequence using the -B option. Details
    are in README.bls.

    5.) The maximum wordsize limit for BLASTN has been removed.

    Bug fixes:

    1.) A problem if the database length, set by the '-z' option was greater than
    2 billion, was fixed.

    2.) A core-dump that resulted from the use of the coil-coil masking
    ('-F C') was fixed by including a file needed for the data directory.

    3.) A bug was fixed that caused some very short alignments to be assigned incorrect
    expect values.

    4.) A bug was fixed that caused formatdb to produce incorrect BLAST databases if
    the input was ASN.1.

    5.) A serious performance problem with BLASTN and longer words (greater than 16)
    was fixed.

    Notes for 2.0.9 release:

    Enhancements:

    1.) two new options have been added to blastall: to produce output in HTML and
    to search a subset of the database based upon a list of GI's.  Please see
    the options section for full information.

    2.) two new options have been added to blastpgp: to produce HTML output and to
    produce an ASCII version of the PSI-BLAST Matrix.  Please see the options section
    for more information.

    3.) formatdb has a new option to allow specification of a 'base' name.  see the options
    section for full details.

    4.) it is possible to mask only during the phase when the lookup table is being built,
    but not during the extensions.  See the options section for full details.

    Bug fixes:

    1.) a problem that occurred when too many HSP's aligned to the same part
    of the query from one database sequence has been fixed.

    2.) a problem that caused seedtop to not perform pattern-matching for DNA
    sequences has been fixed.

    3.) the number of HSP's saved for ungapped BLAST and tblastx is now limited to
    200 to prevent problems with memory and speed.

    4.) a missing thread join that caused problems under DEC Alpha has been added.

    5.) a formatting problem with the database summary at the beginning of the
    BLAST output (if multiple databases totaling over 2 Gig) has been fixed.

    6.) a bug in formatdb that caused a core-dump if the total number of sequences was an
    exact multiple of 100000 was fixed.

    Notes for 2.0.8 release:

    Enhancements:

    1.) Frame and strand information was added to the output.  Examples of the
    new output format may be found at http://www.ncbi.nlm.nih.gov/BLAST/example.html.

    2.) An option that specifes the query strand to be searched (for blastn, blastx, and tblastx)
    has been added.  The option is '-S'.

    Bug fixes:

    1.) The problem with the 'too-wide' parameter input screen under NT was fixed.

    2.) BLAST no longer core-dump's when the query is NULL.

    3.) BLAST no longer core-dump's when the query contains an '@' and blastx or tblastx is selected.

    Notes for 2.0.7 release:

    Bug fixes:

    1.) BLAST now multi-threads properly under LINUX.

    2.) A problem with very redundant databases and psi-blast was fixed.

    3.) A problem with the formatting of the number of identities and positives
    was fixed.  This affected results on the minus strand only and did not
    affect the expect value or scores.

    4.) A problem that caused tblastn to core-dump very occassionally was corrected.

    5.) A problem with multiple patterns in PHI-BLAST was fixed.

    6.) A limit on the number of HSP's that were saved (100) was removed.

    Notes for 2.0.6 release:

    Enhancements:

    1.) PHI-BLAST is included in this release.  Please see notes on PHI-BLAST for
    details.

    2.) SEG has become an integral part of the NCBI toolkit and it is no longer necessary
    to install it separately.  It is also now supported under non-UNIX platforms.

    3.) Access to filtering options.

    If one uses "-F T" then normal filtering by seg or dust (for blastn)
    occurs (likewise "-F F" means no filtering whatsoever).  The seg options
    can be changed by using:

    -F "S 10 1.0 1.5"

    which specifies a window of 10, locut of 1.0 and hicut of 1.5.  One may
    also specify coiled-coiled filtering by specifying:

    -F "C"

    There are three parameters for this: window, cutoff (prob of a coil-coil), and
    linker (distance between two coiled-coiled regions that should be linked
    together).  These are now set to

    window: 22
    cutoff: 40.0
    linker: 32

    One may also change the coiled-coiled parameters in a manner analogous to
    that of seg:

    -F "C 28 40.0 32" will change the window to 28.

    One may also run both seg and coiled-coiled together by using a ";":

    -F "C;S"

    4.) BLAST has been changed to reduce the number of redundant hits that a user
    may see.  This is acheived by keeping track of the number of hits completely
    contained in a certain region and eliminating those lower scoring hits that
    are redundant with others.  This behavior may be controlled with the -K and -L
    options:

      -K  Number of best hits from a region to keep [Integer]
        default = 50
      -L  Length of region used to judge hits [Integer]
        default = 20

    Setting -K to zero turns off this feature.  This is the default only on blastall.

    Bug fixes:

    1.) There was a problem with the procedure that called the external utility seg.
    The need to fix this was obviated by the integration of seg into the toolkit.
    This showed up under LINUX.

    2.) There was a memory problem with formatdb that has been fixed.  This showed up
    mostly under NT and LINUX.

    3.) A problem with running in multi-processing mode under IRIX6.5 (as a non-root user)
    was fixed.

    Notes for 2.0.5 release:

    Enhancements:

    1.) The BLAST version is printed by formatdb in it's log file.

    2.) Multi-database searches no longer require that the -o option be used when
    preparing the databases (i.e., with formatdb).

    Bugs fixed:

    1.) A serious bug with multi-database iterative searches was fixed (thanks to
    Steve Brenner for providing an example).

    2.) 'lcl' is not formatted in the BLAST report when the sequence identifier
    is a local identifier or does not contain a bar ("|").

    3.) A large memory leak in formatdb was fixed.

    4.) An unnecessary cast that caused formatdb to fail on Solaris 2.5 machines
    if the binary was made under 2.6 was fixed.

    5.) Better error checking was added to protect against core-dumps.

    6.) Some problems with the sum statistics treatment of the blastx and tblastn
    programs reported by D. Rozenbaum were fixed.  The number of alignments
    involved in a sum group was misrepresented.  Also the incorrect length for
    the database sequence was used, sometimes casuing a slight change in the
    value reported.

    7.) A problem with blastpgp was fixed that reported incorrect values for
    matrices other than BLOSUM62 during iterative searches.

    Notes for 2.0.4 release:

    Enhancements:

    1.) multiple database searches:

    Version 2.0.4 will accept multiple database names (bracketed by quotations).
    An example would be

                  -d "nr est"

    which will search both the nr and est databases, presenting the results as if one
    'virtual' database consisting of all the entries from both were searched.   The
    statistics are based on the 'virtual' database.

    2.) new options:

      -W  Word size, default if zero [Integer]
        default = 0
      -z  Effective length of the database (use zero for the real size) [Integer]
        default = 0

    3.) The number of identities, positives, and gaps are now printed out before the
    alignments for gapped blastx, tblastn, and tblastx.  Additionally this feature is
    now also enabled for ungapped BLAST.

    4.) Formatdb now accepts ASN.1, as well as FASTA, as input.

    Bugs fixed:

    1.) In blastx, tblastn, and tblastx a codon was incorrectly formatted as a start codon in
    some cases.

    2.) The last alignment of the last sequence being presented was incorrectly dropped
    in some cases.  This change could affect the statistical significance of the last database
    sequence if the dropped alignment had a lower e-value than any other alignments from the
    same database sequence.