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JSpecies News

[March 12th, 2010]

JSpecies V1.2.1 released

A new version of JSpecies is available. Please check the download section.

Mac OS user reported problems with the resolution of the user defined nucmer path. These problems have been fixed in this version.

[December 15th, 2009]

Local sequence identifier 'lcl|identifier' issue

FASTA files enclosing a Local Sequence identifier 'lcl|identifier' are currently not working in JSpecies V1.2 for ANIb calculations. A workaround is to search and rename 'lcl' by 'gnl' (General database identifier) or to delete the identifier complete, which avoids this issue. Calculations with 'lcl' enclosing identifiers do not show the alignment icon in the ANIb overview tab and strange alignment [%] numbers. We expecting a patch in January, don't hesitate to write a email if you have question about.

[November 20th, 2009]

JSpecies V1.2 released

A new version of JSpecies is available. Please check the download section.

In rare cases, it can happen that BLAST is not able to calculate ungapped Karlin-Altschul parameters due to an invalid query sequence. This exception broke JSpecies's ANIb calculations and has been fixed in this version. Thanks for reporting ...

[October 28th, 2009]

JSpecies V1.1 released

A new version of JSpecies is available. Please check the download section.

  • Group close functionality.
    Groups can be opened/closed within a running JSpecies session. No need anymore to relaunch a JSpecies for view a new group.
  • ANIb and ANIm charts changed.
    Instead of a bar chart, JSpecies shows now a histogram.
  • Results coloring in results view.
    Cut off colors are now also shown in the results views.
  • Overview tool tip.
    Results view provides a mouse triggered overview tool tip, shown all available results for a given combination.
  • Several bug fixes and usability enhancements.
    The cross-platform compatibility has been worked out in greater detail and should now theoretical work on all major platforms without errors.

  • [October 24th, 2009]

    JSpecies paper published

    Published online before print, doi: 10.1073/pnas.0906412106.

    [August 7th, 2009]

    JSpecies Version 1.0 released

    Many thanks to the RC testers for reporting bugs and suggesting improvements. Please check the download section.

    [June 9th, 2009]

    JSpecies Version 1.0 RC1

    Today we announce JSpecies first release candidate. Please check the download section. This version has been extensively tested on Ubuntu and is working on Windows machines. Please report bugs. Let's calculate ….

    [June 3rd, 2009]

    JSpecies Webpage Online

    After many hours behind a desk, we are finally happy to be online. The first JSpecies release will follow in a couple of days. If you have comments, question or plaudit/critique for us don't hesitate to contact us under michael.richter(at)uib.es or rossello-mora(at)uib.es .