Converted ExternDefinitions to use sparseArray instead of std::vector
to cut down on required amount of memory when using large sequences
Fix compiler warnings from Ubuntu 12.04 GCC 4.6.1
Fix compile bugs using Ubuntu 12.04 LTS x86_64
Update version number
Fix compile warnings in Windows MinGW GNU 4.7.1
Update version to v0.26
Changing over to autotools from standard makefile
Delete copy of makefile from repository.

makefile is now created using ./configure
Added Makefile to gitignore
Updated dynamic_bitsets to have behavior similar to std::bitset
when using operator[]
Merge branch 'master' into development

Conflicts:
	config.log
	config.status
	src/Makefile
Update authors, copying license, install instructions, and README
Remove makefile located in src folder
Reimplement transitionFuncTraceback function for calling function
when evaluating transition.
Update README.md
Update README.md
Update README.md
Fix misspelling of function names
Merge branch 'master' into development
Added file called LICENSE