Boris Nagaev · Home page | About | Contact | Github | Code | FBB files

NPG-explorer 0.4.0 released

NPG-explorer is a new tool for nucleotide pangenome construction and analysis of closely related prokaryotic genomes.

Version 0.4.0 was released on Jun 12, 2015.

This release has a focus on new developments and a few bug fixes.


  • 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:
  • 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)
    • 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.

This work was presented at ECCB’14 conference: abstract (ru) and poster.