Replace typedef with using statements
Don't dereference containers are empty
Use bit manipulation for faster IUPAC code comparison
Move function to another pair of header and source files
Remove package creation files that moved to a different repository
Remove file path based constructor
Merge branch 'master' into develop
Merge branch 'master' into 4bit
Remove FIRE seeding
Remove unused function
Speed-up: return vectors, not lists
Use plain std::vector instead of boost::ublas::vector for counts
Remove unused struct, and improve code layout
Speed-up: vector based motif and sequence type
Merge branch '4bit' into develop for faster plasma
Merge branch 'master' into develop

Conflicts:
	src/plasma/motif.cpp
Merge branch 'master' into develop
Merge branch 'master' into develop
Make vector output compatible with that of boost
Const char variable for the terminator symbol