JAligner: Java implementation of Smith-Waterman algorithm for sequence alignment

Packages

jaligner	Core classes for the implementation of Smith-Waterman-Gotoh algorithm
jaligner.example	Example for using API of JAligner to perform pairwise sequence alignment.
jaligner.formats	Group of formats for output alignments.
jaligner.matrix	Scoring matrices package.
jaligner.test	Testing package.
jaligner.ui	Command line and graphical user interface.
jaligner.ui.clipboard	Clipboard handling for JNLP and AWT.
jaligner.ui.filechooser	File loading and storing.
jaligner.ui.images	Images used in the toolbar.
jaligner.ui.logging	Logging package.
jaligner.ui.util	Text component utilites package.
jaligner.util	Utility classes for helping core and GUI classes.