PyNAST: Python Nearest Alignment Space Termination tool

PyNAST News and Announcements

Table Of Contents

Installing and using the Mac OS X GUI

Download the draft version of the PyNAST OS X GUI here. Unzip the downloaded file to extract the PyNAST application. Depending on your system settings, the PyNAST application will either be called PyNAST or Ensure that your system meets the requirements listed below. If all requirements are met, double-click on the PyNAST application to launch PyNAST. Note that YOU DO NOT NEED PyCogent or the PyNAST API/command line interface installed to use the PyNAST GUI.

Requirements for the PyNAST GUI

  • An Intel Mac running OS X 10.5 (Leopard).
  • Python 2.5 or greater (but less than Python 3.0) and NumPy 1.3.0 or greater.
  • blastall, formatdb, and bl2seq installed in /usr/bin/, /usr/local/bin/, or $HOME/bin. These are all part of NCBI’s ‘legacy’ BLAST package, NOT the BLAST+ package. Versions 2.2.16 through 2.2.21 have been tested extensively with the PyNAST GUI, but other versions should work. (Due to current limitations of the PyNAST GUI you need to have the required external software installed in one of these specific locations on your system.)

Optional for the PyNAST GUI

  • MUSCLE installed in /usr/bin/, /usr/local/bin/, or $HOME/bin if you want to use that for pairwise aligning.
  • ClustalW installed in /usr/bin/, /usr/local/bin/, or $HOME/bin if you want to use that for pairwise aligning.

Limitations in the draft release of the PyNAST GUI

  • Not all pairwise aligners are available. Missing options are pair_hmm and MAFFT.
  • Users must place external executables in specific locations for PyNAST to find them, rather than PyNAST looking in user-defined locations. This will be addressed by adding a preferences box where users can define where these executables are stored.
  • No help text within the application.