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 18.104.22.168 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.