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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)

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The current proliferation of connected displays and mobile devices from smart phones and tablets to wall-sized displays presents a number of exciting opportunities for information visualization and visual analytics. When a user employs heterogeneous displays collaboratively to achieve a goal, they form what is known as a display ecology. The display ecology enables multiple displays to function in concert within a broader technological environment to accomplish tasks and goals. However, since information and tasks are scattered and disconnected among separate displays, one of the inherent challenges associated with visual analysis in display ecologies is enabling users to seamlessly coordinate and subsequently connect and integrate information across displays. This research primarily addresses these challenges through the creation of interaction and visualization techniques and systems for display ecologies in order to support sensemaking with visual analysis. This dissertation explores essential visual analysis activities and design considerations for visual analysis in order to inform the new design of display ecologies for visual analysis. Based on identified design considerations, we then designed and developed two visual analysis systems. First, VisPorter supports intuitive gesture interactions for sharing and integrating information in a display ecology. Second, the Spatially Aware Visual Links (SAViL) presents a cross-display visual link technique capable of guiding the user's attention to relevant information across displays. It also enables the user to visually connect related information over displays in order to facilitate synthesizing information scattered over separate displays and devices. The various aspects associated with the techniques described herein help users to transform and empower the multiple displays in a display ecology for enhanced visual analysis and sensemaking. / Ph. D.