Well, 0.46 is released. It contains loads of new useful features (The code went through a little beautification as well). Most notably are the following:
-New command line interface. This interface was necessary to really get a convergant matrix very easily.
-Loads of new options available from the command line interface (output matrix precision, assume transitions, scaling factors, and more).... read more
Well, with the 0.38 release I have done a lot of hand testing to verify that the generator does what it is supposed to do. This involves hand calculating everything in a small dataset. This was tedious, but it did lead to the discovery of some errors in the way observed probability was being calculated previously. I feel confident that the calculations are being performed to specifications now. Enjoy the release and make sure to submit any bugs or feature enhancements! ... read more
The last release had two major problems I have discovered. First a bad problem with A residues not being counted. This has been fixed. I also discovered I wasn't counting transitions properly still. This has been fixed as well. In addition to all of this there is new functionality! You can now save your matrices as html. This facilitates easy web display.
Well, I am releasing MatrixGen-0.35. With this release I think we are about ready to move out of Alpha, and call it beta. If anyone downloaded MatrixGen-0.33, you should immediately update to 0.35. MatrixGen-0.33 Had some really interesting bugs which made the statistics generated pretty much random. Those are however fixed, and I think 0.35 is looking pretty good. If anyone finds any problems, hit the bug database.
MatrixGen 0.3 is released. This release focused on two things -- Scalability and accuracy. Memory requirements for large file processing have been drastically reduced. Speed has increased a thousand fold. Files that I could never get to finish processing will now finish in under 10 minutes. The BLOSUM spec as specified by Henikoff and Henikoff is followed exactly now, with the exception of Segment clustering. Segment Clustering support is not currently scheduled.