MEGA

The acronym MEGA stands for Molecular Evolutionary Genetics Analysis, which is the sequence alignment viewer and editor used in phylogenetic analysis and data mining among other applications. Mainly, this software's functions and tools are designed to help scientists and students trace the ancestral origins of different species. Users drag and drop branches into the topology editor when they create phylogenetic trees of proteins. Researchers make use of scripts and external applications that connect to MEGA's computational core through a command line interface. This helps scientists automate the analyses of a large number of multiple sequences. The editor's toolbar menu has been updated to include more formatting options and provide a direct access to notation tools, linear modeling modules and statistical analysis methods. The MEGA version for Macintosh requires the X11 program that came with the Mac OSX Leopard installation package.

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BSEdit

BSEdit is a Windows-based viewer and WYSIWYG editor of protein alignments and DNA/RNA sequences. This multiple sequence alignment tool can open and edit project files and export them to ClustalW, Fasta, Phylip, PIR, NEXUS, GCG, and MEGA file formats. The software can handle simultaneous views and edits of large multiple sequences displayed in separate windows. Users may want to edit alignments manually or use the drag-and-drop function to rearrange sequences. BSEdit runs on the Windows OS, but WinXP users must install .NET Framework 3.0 into the system first before they can use it. The editor saves annotations and comments into the project file and supports single sequence and whole alignment edit modes. In particular, this software can perform a comparative analysis on a specific region in a sequence to check its variation patterns. It also applies circular adjustments on genome alignments.

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