![]() Java creates an additional layer of software (including additional memory consumption) and modern browsers enforce much more caution in running Java applets to avoid security threats. However, in recent years there has been a gradual move away from using Java applets in web development. The latter responds to the need for web site developers to be able to embed MSA visualization. Probably the most popular of the available tools is Jalview 13 which is available in two versions: a standalone Java application which provides many tools and facilities, and as a ’light’ version (JalviewLight) - a Java applet that can be embedded in a web page. A more complete list of MSA viewers is available on the web at. CLC Viewer is a recent free package written in Java which contains a number of integrated tools and acts as a core product for adding other features through a commercial version. Like early versions of CINEMA, PFAAT is implemented in Java for operating system independence. More recent developments include the Protein Family Alignment Annotation Tool (PFAAT) 12 designed specifically for family analysis and incorporating residue annotation tools as well as integration with Jmol for protein structure display. 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.
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