This application software system of Tree Alignment and Reconstruction (TAAR) is an X Window based interactive system developed mainly for sequence analysis. It provides a user-friendly graphical interface and convenient operations for performing Pairwise Alignment, 3-Star Alignment, Phylogeny Reconstruction and Generalized Tree Alignment algorithms. The algorithms for Phylogeny Reconstruction and Generalized Tree Alignment are designed based on heuristic stepwise addition and internal node sequence alignment induction methods. All above algorithms are space-efficiently implemented. For each algorithm, both fast and optimal versions are provided for user's convenience. TAAR can be used for DNA, RNA and PROTEIN sequences analysis. In general, as long as the sequence characters are in the range of a-z and A-Z, and the score matrix alphabet contains the sequence alphabet, the sequence would be accepted by this application and all calculations could be carried out. This software system is programmed in C, Motif and X Window Library functions. It is intended to be running in a UNIX and X Window environment. / Thesis / Master of Science (MS)