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In the initial stage of sequence analysis, a biologist is first faced with the questions about how to choose the best tool to align sequences of interest and how to analyze and visualize the alignment results, and then with the question about whether unaligned regions produced by the tool are indeed not homologous or are just results due to inappropriate alignment tools or scoring systems used. In this paper, we present a versatile alignment visualization system, called SinicView, (for sequence-aligning innovative and interactive comparison viewer), which allows users to efficiently compare and evaluate assorted alignment results obtained by different tools. SinicView calculates similarity of the alignment outputs under a sliding window using the sum-of-pairs method and provides scoring profiles of each set of aligned sequences. Combined with the annotations information, the user can visually compare alignment results either in graphic scoring profiles or in plain text format of the aligned nucleotides. With SinicView. users can use their own data sequences to compare various alignment tools or scoring systems and select the most suitable one to perform alignment and sequence analysis. SinicView is avaiable for free download from http://biocomp.iis.sinica.edu/.