What's new in FSA 1.15.7
May 17, 2014
- Minor compilation fix for gcc 4.6
New in FSA 1.15.6 (Jun 28, 2011)
- Minor compilation fix for gcc 4.5.2 (Robert Bradley)
New in FSA 1.15.5 (Aug 11, 2010)
- Use tr1/unordered_set for annealing if available (Robert Bradley)
New in FSA 1.14.5 (Apr 25, 2009)
- Handle "NA" fields in Mercator maps (Robert Bradley)
- Bugfix for automatic available RAM detection for some Linux distributions (Colin Dewey)
- Parallelization and database modes are disabled by default (Colin Dewey)
- Bugfix for strange behavior where all sequences are left unaligned under some older compilers (Colin Dewey)
New in FSA 1.14.4 (Apr 9, 2009)
- Compilation bugfixes for some Linux systems where floor isn't declared (Robert Bradley)
- Added FSA preprint accepted by PLoS Computational Biology (Robert Bradley)
New in FSA 1.14.2 (Mar 24, 2009)
- Updated FSA preprint (Robert Bradley).
New in FSA 1.14.1 (Mar 24, 2009)
- Changed Mercator-related short options to use upper-case letters (Robert Bradley).
- Mercator slicing stuff now assumes a + strand if strand is unspecified; previously implicitly assumed - (Robert Bradley)
- Tiny bugfix for map_gff_coords: --force-entry was accidentally on by default (Robert Bradley)
- Bugfix for GUI compilation on Linux (Colin Dewey)
New in FSA 1.14.0 (Mar 12, 2009)
- Added experimental --tree-weights option.
- Added experimental --load-probs option.
- Changed default behavior when two sequences have no detectable homology; see new option --require-homology.
- New utility program slice_fasta to extract subsequences from FASTA files.
New in FSA 1.13.4 (Feb 7, 2009)
- Bugfix for % ID calculation for sliced alignments
- More intuitive default anchoring options
- Bugfix for hardmasked error after compilation without MUMMER on OS X 10.4
New in FSA 1.13.3 (Jan 15, 2009)
- Bugfix for alphabet case-sensitivity during learning.
New in FSA 1.13.2 (Jan 13, 2009)
- Compilation fixes for g++ 4.4.
New in FSA 1.13.1 (Jan 10, 2009)
- Bugfix and better automated options for --nucprot
New in FSA 1.13.0 (Jan 10, 2009)
- C++ tools for working with FSA-Mercator whole-genome alignments
- Bugfix for softmasking with exonerate
- Completely re-written sequence and alignment representation code
- Use a model with 2 sets, rather than 1 set, of indel states by default
- Turn iterative refinement on by default with an unlimited number of steps
New in FSA 1.12.1 (Nov 28, 2008)
- Source code documentation updated for Doxygen compatibility.
New in FSA 1.12.0 (Nov 24, 2008)
- Perl scripts to interact with FSA / Mercator whole-genome alignments
- Switch to using only ungapped exonerate anchors
New in FSA 1.11.2 (Nov 15, 2008)
- Bugfix for GUI compilation.
New in FSA 1.11.1 (Nov 14, 2008)
- Bugfixes for anchoring with both Mercator & exonerate
- Compilation fixes for g++ 4.4
New in FSA 1.11.0 (Nov 12, 2008)
- gaps stripped from input sequences
- error thrown if 2 alignable sequence are left unaligned due to RAM constraints
- hardmasked sequence is left unaligned by default
New in FSA 1.10.0 (Oct 31, 2008)
- nucprot option and utility programs translate and prot2codon
- Bugfixes for anchoring with both Mercator & exonerate
- Bugfixes for parallelization & database modes
New in FSA 1.09 (Oct 24, 2008)
- Much faster sequence annealing (Robert Bradley, Colin Dewey & Lior Pachter).
- Better memory usage for long sequences (Robert Bradley).
- Optional Mercator constraints (Robert Bradley and Colin Dewey).
- Optional anchoring with exonerate (Robert Bradley).
- GUI can export TIFF images (Robert Bradley).
- gapcleaner fix (Robert Bradley).
- Parallelization mode (Jaeyoung Do and Colin Dewey).
- Database mode (Jaeyoung Do and Colin Dewey).
- Added submitted manuscript as manual.