/common/base/   Amino acids, ptms, residues and etc 
/common/util/  	String utilities, file utilities, and etc
/common/xml/   	Functions for handling xml files   
/console/	      Main functions for topfd, toppic, topmg, and topmerge
/filter/	      Various protein sequence filtering methods
/gui/		        GUI for topfd, toppic, topmg, and topmerge
/merge/         Merging proteoform identifications from several samples
/ms/            Mass spectra, envelops, and features
/prsm/		      Proteoform spectrum matches and related functions
/search/        Various database search algorithms
/seq/     	    Fasta sequences and proteoforms
/spec/    	    Various peaks and spectrum classes
/stat/local/		Charaterization and localization of mass shifts
/stat/mcmc/		  An Markov chain Monte Carlo method for E-value estimation
/stat/tdgf/		  A generation function method for E-value estimation
/suffix/  	    Suffix tree used in the manuscript Deng et al, Bioinformatics 31, 532-538
/visual/	      Functions for visualization of proteoform spectrum matches
