0.5.8

version 0.5.8

0.5.7

version 0.5.7

0.5.6

version 0.5.6

0.5.5

version 0.5.5

Version 0.5.4

Download binary files for your operating system. See links below.

Warning. The installer and the program doesn't work from a directory with Russian letters in name.

0.5.3

version 0.5.3

0.5.2

Release 0.5.2

Bug fixes.

• Fix Windows build
  • Workaround for gcc5 bug
  • Disable LuaJIT explicitly
  • algo_lua.cpp: Lua 5.3 compatibility
  • fix windows build warning
• Fix typos and errors in README and Info's output
• config: do not fail with lua-npge npge.conf

Download binary files for your operating system. See links below.

Warning. The installer and the program doesn't work from a directory with Russian letters in name.

0.5.1

Release 0.5.1

Bug fixes and few improvements.

• Pangenome: join collinear blocks even if bad.
• Fix intermediate fragments joining. This bug was
  introduced in 2c76b51
  (2015-05-16), version 0.4.0 (2015-06-12).
• Update requirements of a good pangenome in README.md
  according to what is implemented now.
• Genes-vs-blocks partition: print only locus_tag.
• GUI: jump to fragment end if there is no gene end.
• Info: print % of NPG for total blocks length.
• Recognize lua-npge format of Fragment id encoding.
• Download compressed files from the database.
• Fix errors in GetData and AddGenes.
• AddGenes: skip repeated locus_tag.
• Fix some build issues on various setups.
• meta_test: ignore directories without script.npge.
• Setup Travis for cross-compiling to Windows (MXE).
• Setup Travis for uploading build artifacts to GitHub.
• Update BLAST in the distribution to 2.2.31.

Download binary files for your operating system. See links below.
Warning: the Windows build doesn't work! Please use Windows files from release 0.5.2.

0.5.0

Release 0.5.0

Bug fixes and few improvements.

• Change alignment requirements.
  • Change meaning and default value of MIN_END.
  • Add option FRAME_LENGTH.
• Add processor CountSMS
• Filter: increase size of gap score table to 1000
• Tools.
  • BLAST version: 2.2.29 -> 2.2.30
  • Option npge -v [--version]
  • Clarify option -g
  • Hide option DEV_NULL from npge.conf
  • GUI: show % of length occupied by low similarity
  • Examine: do not recommend nan identity
• Documentation.
  • ECCB'14: add abstract in English (original)
  • README: meaning of columns of *.bi files
  • README: add blocks types algorithm (image)
• Fix bugs.
  • FreeBSD build fixes. Thanks to Dmitry Marakasov!
  • Fix segfault in PrintPartition.
  • Fix the bug in BlastFinder (crash on empty input).
  • Fix windows x64 build.
  • Do not apply UPX to 64-bit Windows executables.
  • Lua code: compatibility with Lua >= 5.2.
  • Find more locus_tag's in GeneBank files.
  • FindLowSimilar: fix division by zero.

Download binary files for your operating system. See links below.

0.4.0

Release 0.4.0

Improvements:

• Change alignment requirements. Require high similarity in
  every slice of length MIN_LENGTH. Use logarithmic
  gap penalty. Introduce option MIN_END. Do not require
  length of fragment >= MIN_LENGTH.
• Short blocks of one fragment are now called minor blocks.
  All minor blocks are shorter than MIN_LENGTH.
• GUI/BSA: show block's length for global blocks.
• Use Travis CI: https://travis-ci.org/npge/npge
• BlockSet alignment: g-blocks and i-blocks. G-blocks
  are formed from joined consequent s-blocks. S-blocks
  are always aligned in g-blocks. Other blocks form
  i-blocks.
• Speed up SplitRepeats. Improve time complexity by
  building the tree from diagnostic positions. Critical
  for blocks of > 500 fragments.
• PostProcessing produces new files:
  • table of global blocks' properties (*.gbi)
  • blockset alignments with block names (*.blocks)
  • pangenome-small.bi
  • nj-global-tree-full.tre
  • genes/partition.tsv
• Mutations file parser written in Python (example)
• Print local time with timezone offset to logs
• Add descriptions of some algorithms (*.md files)
• Translate ECCB'14 abstract into Russian
• Fix bugs:
  • Fix bugs in GUI
  • Fix bugs in annotations parser (GetData)
  • Fix bugs in local blockset alignment builder. It
    used to consider linear sequences to be circular.

Download binary files for your operating system. See links below.