Release notes for PARALIGN

PARALIGN version 5.0 was released on 9 April 2008

The following issues have been revised in this version compared to version 4.2.2:

• Support for the latest version of preformatted database files from NCBI
• Some bugs have been fixed
• Minor changes in the output formats
• Code has been rewritten substantially but it has also been extensively debugged, and is believed to perform better than the previous version.

PARALIGN version 4.2.2 was released on 11 May 2006

The following issues have been revised in this version compared to version 4.2.1:

• Support for Linux on PowerPC has been included.
• Bugs have been fixed

PARALIGN version 4.2.1 was released on 24 March 2006.

The following issues have been revised in this version compared to version 4.2.0:

• A bug related to a segmentation fault appearing in some cases with many multiple queries has been removed.
• A bug related to the names of alias files has been removed.

PARALIGN version 4.2.0 was released on 3 March 2006.

The following issues have been revised in this version compared to version 4.1.0:

• Alias files and command line options for searching database subsets based on gi number lists or taxid number lists have been implemented. This allows the direct use of all the preformatted databases distributed by NCBI.

PARALIGN version 4.1.0 was released on 12 January 2006.

The following issues have been revised in this version compared to version 4.0.0:

• Memory leak problems have been fixed.
• Alias files (.pal, .nal) incorporating database subset masks are implemented.

PARALIGN version 4.0.0 was released on 23 October 2005.

The following issues have been revised in this version compared to version 3.4.3:

• The use of concatenated databases in the form of simple "alias" files has been implemented. This makes it easy to search very large databases that have been split into pieces in order to avoid file system limitations.
• A bug that affected nucleotide searches with the ParAlign algorithm on Pentium 4-type processors have been fixed. The error made the software slow because an unnecessary high number of Smith-Waterman-comparisons were made. The actual results were not affected in any negative way.
• A bug that occured with databases without a name has been fixed.

PARALIGN version 3.4.3 was released on 28 April 2005.

The following issues have been revised in this version compared to version 3.4.1:

• Multiple query sequences are accepted. The tab-separated plain text output now includes the query description.
• Problems with long lines (>1024 characters) in query sequence files fixed. Arbitrarily long lines are now properly handled.
• Optional XML formatted output (experimental, may be changed without notice)
• Another score matrix for RNA-RNA hybridizations added (highly experimental)

PARALIGN version 3.4.1 was released on 18 October 2004.

The following issues have been revised in this version compared to version 3.3.7:

• Performance improvements in database sequence reading.
• Score matrix for RNA-RNA hybridizations added. (Highly experimental.)
• Version number now shown in help and error messages.
• Part 8(e) of the license has been removed.
• Issues with "-s" parameter fixed.
• Some issues with very large databases fixed.
• Problems with long lines (>511 characters) in query sequence files fixed. Lines up to 100 000 characters are now properly handled.

PARALIGN version 3.3.7 was released on 28 January 2004.