code Directory Reference

Files
	common.cpp
	This file contains common utility functions used in the MSA project.
	common.h
	This file contains declaration of common utility functions used in the MSA project.
	converter.cpp
	MSA File Converter.
	flagHandler.cpp
	This file contains the implementation of the FlagHandler class.
	flagHandler.h
	This file contains the declaration of the FlagHandler class.
	msaReader.cpp
	This file contains the implementation of the MSAReader class and its derived classes.
	msaReader.h
	This file contains the declaration of the MSAReader class and its derived classes.
	msaWriter.cpp
	This file contains the implementation of the MSAWriter class and its derived classes.
	msaWriter.h
	This file contains the declaration of the MSAWriter class and its derived classes.
	multimerHandler.cpp
	This file contains the implementation of the MultimerHandler class to manage and manipulate MSA of a multimer.
	multimerHandler.h
	This file contains the declaration of the MultimerHandler class to manage and manipulate MSA of a multimer.
	neff.cpp
	Neff Computation.