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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
* has been updated. It is still a work in progress.
Version 1.0
* Initial Release
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