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Commits on Jan 5, 2011
  1. Adding example alignments

    wash committed Jan 5, 2011
Commits on Aug 25, 2010
Commits on Jan 7, 2010
  1. Fix documentation.

    wash committed Jan 7, 2010
Commits on Dec 1, 2009
  1. Updating version information.

    wash committed Dec 1, 2009
Commits on Oct 21, 2009
  1. Merge branch 'gh-pages' of git@github.com:wash/rnacode

    Stefan Washietl committed Oct 21, 2009
  2. Updated documentation in README file.

    Stefan Washietl committed Oct 21, 2009
Commits on Oct 7, 2009
  1. Most of the color coding finished. Has still

    Stefan Washietl committed Oct 7, 2009
    some rough ends and needs more testing.
Commits on Sep 15, 2009
  1. Started postscript coloring again.

    Stefan Washietl committed Sep 15, 2009
Commits on Jul 16, 2009
  1. Fixed subtle bug in algorithm to get HSS. Now HSS are extended

    Stefan Washietl committed Jul 16, 2009
    as far as possible on both ends also with neutral sites of score 0.
Commits on Jul 8, 2009
  1. Add BLOSUM90 to see if this makes any difference at all.

    Stefan Washietl committed Jul 8, 2009
  2. New options "--best-region" and "--best-only"

    Stefan Washietl committed Jul 8, 2009
  3. Added Peter's sequence weighting code (not active yet).

    Stefan Washietl committed Jul 8, 2009
Commits on Jul 5, 2009
  1. Fixed memory leak and added explicit error handling when

    Stefan Washietl committed Jul 5, 2009
    EVD fit fails.
Commits on Jul 2, 2009
  1. Fix a major bug causing bad and frequent segfaults.

    Stefan Washietl committed Jul 2, 2009
Commits on Jun 29, 2009
  1. Some documentation for README file.

    Stefan Washietl committed Jun 29, 2009
Commits on Jun 26, 2009
  1. Implement --best-only feature; handle Ns; bump version number to 0.2b…

    Stefan Washietl committed Jun 26, 2009
    …eta;
Commits on Jun 25, 2009
  1. Implemented 'stop-early' feature. This avoids calculating the exact

    Stefan Washietl committed Jun 25, 2009
    p-value if its verly likely to be above the specified cutoff.
  2. Writing some documentation.

    Stefan Washietl committed Jun 25, 2009
Commits on Jun 24, 2009
  1. github generated gh-pages branch

    wash committed Jun 24, 2009
Commits on Jun 23, 2009
  1. Improved efficiency of calculation of the background model which

    Stefan Washietl committed Jun 23, 2009
    is apparently the major bottleneck for short alignments.
  2. Cleaning and preparing for distribution.

    Stefan Washietl committed Jun 23, 2009
Commits on Jun 19, 2009
  1. Significant speedup (2-3x), crash fixes and cleaning up.

    Stefan Washietl committed Jun 19, 2009
Commits on May 29, 2009
  1. Removed unneccessary function calls from inner loop. Is now 30% faster

    Stefan Washietl committed May 29, 2009
    but still slower than expected.
Commits on May 28, 2009
  1. Explicit penalizing stop codons.

    Stefan Washietl committed May 28, 2009
Commits on May 27, 2009
  1. Statistics should be correct again now. Unfortunately it is even

    Stefan Washietl committed May 27, 2009
    slower now.
Commits on Apr 30, 2009
  1. Backtracking and testing code.

    Stefan Washietl committed Apr 30, 2009
Commits on Apr 29, 2009
  1. Needed to fix all memory leaks before we can go on with testing on re…

    Stefan Washietl committed Apr 29, 2009
    …al alignments.
Commits on Apr 23, 2009
  1. Removed unnecessary function call in inner loop which made this cubic;

    Stefan Washietl committed Apr 23, 2009
    Scan both forward and reverse complement.
  2. Rewritten most of the code support the new gap-model.

    Stefan Washietl committed Apr 23, 2009
Commits on Feb 1, 2009
  1. More work on postscript output.

    Stefan Washietl committed Feb 1, 2009
Commits on Jan 29, 2009
  1. Changed algorithm that not average of every sequence against every other

    Stefan Washietl committed Jan 29, 2009
    sequence is used, but only the comparison between the first which each
    other. Benchmarks shows that this gives exactly the same results but
    is much faster (because it is linear with species number not quadratic)
Commits on Jan 21, 2009
  1. Removed TODO from Makefile.am

    Stefan Washietl committed Jan 21, 2009