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There are many web-based multiple sequence alignment services accessible around the world. However, many researchers working on biological sequence analysis still struggle with inefficient, unfriendly user interface, and limited capability multiple sequence alignment software. In this study, we provide a comprehensive survey of regional and continental facilities that provide web-based alignment services. We also analyze and identify much needed services that are not available through these existing service providers. We then implement a web-based model to address these needs. From that perspective, our web-based multiple sequence alignment server, SeqAna, provides a unique set of services that none of these studied facilities have. For example, SeqAna provides a multiple sequence alignment scoring and ranking service. This service, the only of its kind, allows SeqAna's users to perform multiple sequence alignment with several alignment tools and rank the results of these alignments in the order of quality. With this service, SeqAna's users will be able to identify which alignment tools are more appropriate for their specific set of sequences. In addition, SeqAna's users can customize a small alignment sample as a reference for SeqAna to automatically identify the best tool to align their large set of sequences.