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).of Wa subsequence of the query.

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.

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

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:

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:

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.

3.) A volume option ('-v') has been added to formatdb. This option breaks up large
FASTA files int