changelog.txt

Version 1.2
 * Migration from Autoconf/Automake to CMake for building.  Easier to develop
   and build packages for modern operating systems.
 * Bug fix for homoplasious insertions.  In very large trees (>8000 branches)
   the bug can still affect the output in very rare cases.  Email me for instructions
   on avoiding this limitation.
 * All empty columns in the alignment are removed by default.
 * New KeepEmpty variable to preserve empty columns.  GapPlus is true forces
   KeepEmpty to be true.
 * New KeepFlank option to control long deletions into flanking regions.

Version 1.1.2
  * Bug fix in reading root sequence from input file

Version 1.1.1
  * More bug fixes in deletion code

Version 1.1
  * Bug fixes in deletion code
  * Bug fixes in recombination code
  * Portability Fixes
  * Clustal default format
  * New [Header] format
  * New [.SubHeader] format
  * Shorter format names: aln, phy, nex, fas, txt, out, poo
  * Format detection based on output file name
  * Output file can be overriden by "-o filename" flag
  * NexusCode depreciated
  * Out.Block.Head, Out.Block.Before, Out.Block.After, Out.Block.Tail added
  * Varable Substitution enabled for Out.Block.*
  * Out.Subst boolean to turn substitution on and off
  * Getopt library support
  * Quiet mode (disable errors and warnings)
  * Output file commandline override
  * Similiar to python triple quotes specify a multiline strings.
      - Triple double quotes remove initial and final newlines
      - Triple single quotes preserve initial and final newlines
  * Lambda.pl has been updated.  It is still a work in progress.
  
Version 1.0
  * Initial Release