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Version 1.62 2017-08-06 Changes: - Added new column reporting percent coverage of hits with respect to reference sequence. Thanks to Konstantin Kuleshov for this request. WARNING! BACKWARDS INCOMPATIBILITY: the additional data column is inserted as label4 before the percent identity column, so label numbers 4 through 6 are now 5 through 7. - Added new '-keepinserts on|off' option for BLAST to preserve hit insertions relative to the query. This is useful when dumping a search to an unaligned output format (fasta, pir) and the full length HSPs are needed. Note: the default behaviour is to cut hit insertions to make the query contiguous. Thanks to Andrea Luchetti at Uni. Bologna for this request. - Added/moved column header information to ruler line in default and html output modes; changed default behaviour to display ruler (-ruler on is now the default). - Changed percent identity filtering from all pairwise comparisons to simple pairwise comparison with reference row. WARNING! BACKWARDS INCOMPATIBILITY: changes meaning of '-minident' and '-maxident' options. Colouring: - Changed to allow 'find' colouring independently of 'alignment' colouring, so both can be applied (formerly 'find' colouring overrode any other). Thanks to Konstantin Kuleshov for this request. - Added single colour colormap capability to consensus line colouring. Input formats: - Updated to handle BLAST 2.6.0+ '-outfmt 7' changes. Output formats (clustal, fasta, msf, pir, plain, rdb): - Added percent coverage, percent identity to output format converters. - Added search row number to output format converters as a prefix to the sequence identifier: 0:test (query row) 8:emb|AL021726|DMC171E4 (search hit 8) 8.2:emb|AL021726|DMC171E4 (search hit 8, discrete HSP 2). - rdb output mode now reports search query as row 0 (was empty before). Bugs fixed: - Fixed bug in output format converters that replaced unknown 'X' residues in blast query with gaps. - Fixed bug in propagation of symcolor and gapcolor options in the absence of an explicit coloring scheme. - Fixed bug in minident/maxident truncating search listings.
Source: README.txt, updated 2017-08-06

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