JAligner: open source Java implementation of Smith -- Waterman. An open source Java implementation of the Smith-Waterman algorithm with Gotoh’s improvement for biological local pairwise sequence alignment using the affine gap penalty model. Features: The space complexity to perform the dynamic programming with the main similarity scores matrix and the 2 auxiliary gaps matrices is reduced from O(m×n) to O(n), where m and n are the sizes of the vertical sequence and horizontal sequence respectively, by using sufficient single-dimensional arrays of size n instead of the original two-dimensional arrays of size m×n. The two-dimensional array of size m×n, for holding the traceback directions (diagonal, left, up and stop), is mapped into a single-dimensional array of size m×n. This approach speeds up the process of memory allocation because the Java Virtual Machine (JVM) attempts to allocate a single-dimensional array of m×n ”bytes” (primitive data type), instead of attempting to allocate an array of m ”objects”, each of which is an ”array” of n bytes. In addition to the 70 already included scoring matrices, which have been picked up from the NCBI site, JAligner works with user-defined scoring matrices. It is easy to use JAligner through a friendly Graphical User Interface (GUI), simple command line syntax or reusable Programming Application Interface (API).