STAMP version history

From Bioinformatics Software
Jump to navigationJump to search

The version history is now at GitHub.


  • Added support for BIOM profiles.
  • Updated manual.


  • Added group and multi-group heatmaps.
  • Improved speed of table updates.
  • Bug fix: Multi-group bar plots were incorrectly scaled by 100.

v2.0.0 (release candidate 6)

  • STAMP profiles with 'unclassified' taxa are now handled properly.
  • Improved handling of degenerate cases where parent categories have no sequences assigned to them.

v2.0.0 (release candidate 5)

  • Added compatibility with MG-RAST LCA profiles.

v2.0.0 (release candidate 4)

  • Added option to PCA plots to assign each group a unique shape.
  • Fixed issue with MG-RAST profiles. These profiles do not form a strict tree as required by STAMP. A strict tree structure is now enforced by modifying category names that appear multiple times.
  • Fixed processing of mothur classify.seqs() results that was causing an error for certain reference taxonomies.
  • Fixed bug causing PCA plots to generate an error under some circumstances when clicking on points to determine sample IDs

v2.0.0 (release candidate 3)

  • Fixed generation of 'two groups' PCA plots along with various OS X related bugs

v2.0.0 (release candidate 2)

  • Fixed bug where STAMP fails due to calculating PCA on a singular matrix.

v2.0.0 (release candidate 1)

  • Initial official release of STAMP version 2.


  • Provides support for the new functional and organism profiles in MG-RAST v3.0.


  • Exploratory scatter plots now support histogram summaries of the distribution of features.
  • x-axis labels of relevant plots can now be modified to accommodate profiles where feature counts do not originate from sequences.
  • Multi-code COGs can now be treated as separate features or a sequence can be assigned to each COG code.
  • Fixed issue with OS X installation which caused the data files required for COG annotations to be missing.
  • Fixed bug leading to an infinite loop of error messages when trying to generate excessively large plots.
  • Fixed bug causing cursor to remain as a "busy" cursor after configuring a plot.


  • Any Python generated error is now displayed to the user to aid in debugging file format issues or reporting possible bugs.
  • Extra blank lines in profile files are now ignored.
  • File menu items now have more descriptive names making their use more transparent.
  • Fixed bug causing the command line execution to produce some output messages even when the verbose option was set to 0.
  • Open profile dialog now shows both *.spf and *.txt files by default.


  • STAMP can now read profile files with Windows, Unix, or MAC style line endings.
  • More informative error messages.


  • Fixed bug with label ordering being reversed in extended error plots (bug introduced in v1.02)


  • Fixed bug resulting in save tables failing (thanks to Mattias de Hollander for bring this to my attention).


  • Fixed bug where last directory was not retained when opening or saving files under Windows XP.
  • Added warning dialogs when about to plot profiles containing several hundred features.


  • Modified code to remove dependency on PyQt4 and matplotlib when running from the command-line.
  • Added unit tests (see


  • Initial release