The project for developing this software was initiated by the leadership of Masatoshi Nei in his laboratory at the Pennsylvania State University in collaboration with his graduate student Sudhir Kumar and postdoctoral fellow Koichiro Tamura.

130) outlining the scope of the software and presenting new statistical methods that were included in MEGA.

The personal computers then lacked the ability to send the monograph and software electronically, so they were delivered by postal mail.

From the start, MEGA was intended to be easy-to-use and include solid statistical methods only.

A command line version, MEGA-Computing Core (MEGA-CC), is available for native cross-platform operation.

The Alignment Editor in MEGA includes an integrated tool for both ClustalW and MUSCLE programs.

All actions take place in the Analysis Explorer, which can be found in the main menu of MEGA.

Once an option is selected, the user can choose either ClustalW or MUSCLE from the Alignment tab located at the top of the page.

To successfully use sequences from NCBI, it is advised to change the searches to FASTA format and use the “Add to Alignment” button.

[8] MEGA's extended format allows users to save all data attributes, such as sequence length, nucleotide positions, gaps, and ambiguous states.

[9] Additionally, MEGA supports data import from other formats, such as Clustal, which ensures a seamless transition between popular file types.

[10] After importing a dataset, MEGA provides multiple different data viewer options.

This allows users to group sequences by a specific characteristic and view subsequent phylogenetic trees.

MEGA offers support for modifying the genetic code used for translating DNA sequences.

Features like columnar block selection-editing aid in the performance of bulk operations, like changing letter case or font size.

Additionally, the editor includes line numbers to assist with the navigation of large files and identifying areas of interest.

MEGA provides a graphical interface for displaying and manipulating aligned nucleotide and protein sequences.

[18] The Sequence Data Explorer has multiple menu functionalities to help with exporting data, searching alignments, changing display features, highlighting sites, and computing statistics: Substitution Models in MEGA allow various options with different attributes of substitution models for both DNA and protein sequences.

MEGA allows a user to conduct an analysis of the data with a specified value of R. A key takeaway is when R equals 0.5, it means there is no bias towards either a transition or transversion substitution.

MEGA offers a wide variety of options for calculating evolutionary distance between a pair of nucleotide or amino acid sequences with or without standard errors.

In addition, every distance method provides options for handling gap and missing data, and codon position if applicable.

Key factors to determine which selection the output will be is the variances of the synonymous and nonsynonymous sites.

[34] The molecular clock hypothesis suggests that all sequences have evolved at a constant rate over time.

Therefore, the molecular clock test evaluates this statement in conjunction with the data provided by the user.

If the resulting numbers differ by a large factor, the molecular clock hypothesis may not be valid for the given data set.

MEGA provides a graphical interface for displaying a phylogenetic tree based on a variety of options.

In the view menu, the tree can be displayed in three different styles: traditional, radiation, or circle.

The view menu also offers toggling topology scaling, changing font type and size, arranging taxa, showing/hiding various details, and a general option for more control over the tree drawing aspects.

Other export options include the current timetree calibrations, analysis summary, partition list, and pairwise distances.

The image format supported are BMP, PNG, PDF, SVG, TIFF, and EMF.