![]() Clustal Omega is the most recent version, but at the time of writing only has a command line interface - a beta version of a GUI is due to be released soon. Other software includes MPSA 9, ANTHEPROT 10 and ClustalX 11, a GUI for the ClustalW multiple sequence alignment program, providing an integrated environment for aligning sequences and analyzing results. It has now been rewritten in C++ and is part of UTOPIA 8. CINEMA 7 was probably the first sequence alignment viewer and editor implemented in Java, a platform independent programming language allowing graphical user interfaces (GUIs) to run on any operating system. A problem in writing graphical software is the operating-system dependency of many graphics libraries. Other early viewers include GeneDoc 3, BioEdit, Seaview 4 and DCSE 5 which is part of the RnaViz package for visualizing RNA secondary structures 6, but which can be used for protein sequence alignments. Neither seems to be actively maintained or easily available any more. Two of the earliest tools were HOMED 1 and MALIGNED 2 written for VAX/VMS workstations. ![]() These range from tools which provide attractive printed outputs, through standalone graphical tools - either operating-system dependent, or independent - to web-based viewers. As a result, there are a plethora of tools for viewing MSAs. Viewing multiple sequence alignments (MSAs) is a fundamental requirement in the analysis of protein sequences, allowing us to visualize conservation across protein families as well as unusual features of particular sequences.
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