Version 1.67 2020-02-14

Changes:

• Added PHIBLAST parser for BLAST+
• Added cross-platform installer script 'install.pl'
• Added 'Makefile.PL' as alternative installer

Input formats:

• Tested with BLAST 2.10.0+
• Tested with FASTA 36.3.8h [2020-02 build]

Bug fix:

• MS Windows gave parse error and lost initial alignment lines when reading
  from stdin.

Version 1.66 2019-09-01

Version 1.66 2019-09-01

Changes:

• Added '-sort cov | pid | cov:pid | pid:cov' option to resort sequences by
  (1) coverage, (2) percent identity, (3) coverage then percent identity,
  (4) percent identity then coverage, with respect to the reference
  sequence.

Input formats:

• Tested with BLAST 2.9.0+
• Tested with FASTA 36.3.8h [2019-08 build]

Bug fix:

• FASTA 36 parser omitted database hits with very short identifiers.

Version 1.65 2019-04-22

Version 1.65 2019-04-22

• Speed improvement.
• MAF format now outputs all blocks instead of just the first.
• Format conversions add newline between separate alignment blocks.

Input formats:

• Tested with BLAST 2.8.1+
• Tested with FASTA 36.3.8g [2018-10-23 build]

Bug fixes:

• Replaced option range processing 1..N, lost in version 1.63.

Other:

• Refactoring of parsers.

Version 1.64 2018-05-14

Version 1.64 2018-05-14

Input formats:

• Tested with BLAST 2.8.0+ (alpha version)

New features:

• Speed improvement.

• Added '-sequences on|off' option to disable processing and output of
  sequences for faster analysis (issue #13).

• Added pass-through of extra 'blast -outfmt 7' sbjct fields (staxid,
  ssciname, scomname, sblastname, sskingdom, staxids, sscinames, scomnames,
  sblastnames, sskingdoms). These can be switched off using new label
  control option '-label8' (issue #14).

Bug fixes:

• Fixed regression in output format conversion since v1.62, whereby
  unaligned input sequences were truncated instead of being passed through
  unchanged.

Other:

• Complete rewrite of display mechanism.
• Ongoing refactoring.

Version: 1.63 2018-03-25

Version: 1.63 2018-03-25

Input formats:

• Tested with BLAST 2.7.1+
• Tested with FASTA 36.3.8f, 36.3.8g

Changes:

• Changed option '-width flat' to '-width full'.
  WARNING! BACKWARDS INCOMPATIBILITY: the default setting, so probably not
  an issue.
• Changed name of output format '-outfmt new' to '-outfmt mview'.
  WARNING! BACKWARDS INCOMPATIBILITY: the default setting, so probably not
  an issue.

New features:

• Added "comment" mode for rows starting with hash, '#'.
• Added "comment" row colouring mode that reads a colormap name embedded in
  the row comment identifier, like '#DSSP:id'
• Added 'DSSP' colormap for protein secondary structure rows.
• Added GNU-style '--' end of command line options flag.

Bug fixes:

• Fixed undefined variable warnings when using '-groupfile' option.
• Fixed JNETZ parser warnings.
• Fixed JNETZ reporting colours even when no colouring set.
• Fixed clustal conservation line bug losing some '.' symbols.

Other:

• Complete rewrite of option parsing mechanism.
• Ongoing refactoring.

Version 1.62 2017-08-06

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.

Version 1.61 2016-11-14

Version 1.61 2016-11-14

• Added '-coloring mismatch' mode, which behaves like '-coloring identity',
  but highlights the mismatches instead of the identities. Using this you
  can see blocks of misalignment and individuate particular misaligned
  residue types by colour. Requested by Andrew Davis.
• Changed colormap and consensus group 'mismatch' pattern from '*' to '.':
  (1) if you use your own colormaps or consensus maps, the wildcard
  effect in a colormap map is now obtained with . instead of *, and (2)
  the * character now explicitly matches * in the input sequences
  (typically a translated stop codon) so these can now be coloured
  independently like a normal residue.
• Added colouring by single named colour; added X11 and Web 4.0 colours:
  list them with 'mview -listcolors'.
• Updated to handle BLAST 2.5.0+ change in '-outfmt 7' standard field names:
  'query /sbjct id' became 'query/sbjct acc.'
• Tested with BLAST 2.4.0+, 2.5.0+, FASTA 36.3.8e.

Version 1.60.1 2015-10-13

Version 1.60.1 2015-10-13

• Fixed error in get_hsp_groups calling keys(); affects BLAST, but only
  triggered under older versions of perl (seen with 5.10, fine with 5.18).

Version 1.60 2015-10-09

• Changed HTML output to HTML5: added DOCTYPE html, removed FONT tags.
• Added BLAST+ PSIBLAST parser.
• Added BLAST+ '-outfmt 7' support.
• Changed BLAST '-hsp discrete' mode to always set HSP count, N = 1.
• Fixed 'plain' output format to not truncate long identifiers.

Version 1.60 2015-10-09

Version 1.60 2015-10-09

• Changed HTML output to HTML5: added DOCTYPE html, removed FONT tags.
• Added BLAST+ PSIBLAST parser.
• Added BLAST+ '-outfmt 7' support.
• Changed BLAST '-hsp discrete' mode to always set HSP count, N = 1.
• Fixed 'plain' output format to not truncate long identifiers.

Version 1.59 2015-07-17

Version 1.59 2015-07-17 (GitHub)

• This is a re-release with only documentation changes.
• Code base moved to GitHub.

Version 1.59 2015-07-06 (SourceForge)

• 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 search 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 5.22.0.1 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.