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Version 1.59 2015-07-06 Improved algorithm for assembly of alternative search alignment fragments with stricter constraints on selection of fragments that maintain query and hit sequence orderings; affects all BLAST and FASTA searches when the number of seach result fragments is greater than 1. Changed BLAST scoring information to report number of HSPs, best score and significance for the HSPs used in the assembly, rather than those stated in the parsed BLAST ranking; affects all BLAST searches. Updated FASTA parsers to recognise '>--' alternative alignments. Added FASTA family support for TFASTM, TFASTF, TFASTS (experimental). Modified code to work on Windows: fixed problems with filepaths containing backslashes; added low-level handling of line endings to allow UNIX (LF) and Windows/DOS (CRLF) data files to be read on either system. Tested with Strawberry Perl 64bit under Wine. Fixed bug in CLUSTAL conservation line that sometimes miscalculated column positions; affects BLAST and FASTA searches. Fixed bug in PIR output that inserted wrong terminal gap character. Fixed bug in percent identity calculation: now case-insensitive and treats unknown 'X' characters as mismatches. Fixed bug in FASTA/Pearson parser that could skip description field. Major refactoring of components and discontinued CVS on SourceForge.
Source: README.txt, updated 2015-07-07