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list of sequence alignment software This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins. Database searc ...

. Multiple alignment visualization tools typically serve four purposes: * Aid general understanding of large-scale DNA or protein alignments * Visualize alignments for figures and publication * Manually edit and curate automatically generated alignments * Analysis in depth The rest of this article is focused on only multiple global alignments of homologous proteins. The first two are a natural consequence of most representations of alignments and their annotation being human-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature. The third is necessary because algorithms for both ''

multiple sequence alignment Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutio ...

'' and ''

structural alignment Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RN ...

'' use heuristics which do not always perform perfectly. The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.

Alignment viewers, editors

Alignment viewers, editors

See also