add tycoon stuff to include path so including cactus doesnt break anything
convert iupac weirdo code letters to n and spit warning when converting sequences
merge development
Making FASTA reader handle FASTA comments and probably newlines
Merge pull request #3 from adamnovak/master

Making FASTA reader handle FASTA comments and probably newlines
Merge branch 'master' of https://github.com/glennhickey/cactus2hal into development

Conflicts:
	src/fastaReader.cpp
Adding some more informative error messages for things like EOF.