The main window in MEGA contains a menu bar, a main toolbar (just beneath the menu bar), a secondary toolbar near the bottom of the window, and a bottom status bar.
Menu Bar
Menus: Description
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File |
Use the File menu commands to open data for analysis, edit text files, convert file formats, and exit MEGA. |
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Analysis |
Use the Analysis menu to launch the analyses available in MEGA. |
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Help menu |
Use the Help menu to access the online help system, which is displayed in a special help window. |
Main Toolbar
This toolbar contains logically organized menus for launching the analyses available in MEGA as well as for importing/exporting data.
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Align |
Edit and build sequence alignments, view/edit sequencer files, query online data banks, do BLAST search, and launch the MEGA Web Browser. |
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Data |
Open data and session files, explore active data, export active data, save active data to a session file, select genetic code table, select/edit genes and domains, select/edit taxa and groups. |
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Models |
Launch analyses related to substitution models, such as best-fit model selection, pattern heterogeneity tests, estimation of substitution matrix and transition/transversion bias, calculate codon usage bias and composition statistics. |
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Distance |
Compute evolutionary distances: pairwise, overall mean, within group mean, between group mean, and net between group mean. |
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Diversity |
Compute mean diversity: within sub-populations, in entire population, between populations. Also, compute coefficient of differentiation. |
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Phylogeny |
Construct/test phylogenies using Maximum Likelihood, Maximum Parsimony, Neighbor-Joining, Minimum Evolution, and UPGMA. Also, open saved tree sessions. |
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User Tree |
Analyze a given tree using Maximum Likelihood, Maximum Parsimony, or Ordinary Least Squares. Display Newick trees, or edit/draw trees manually. |
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Ancestors |
Infer ancestral states using Maximum Likelihood or Maximum Parsimony. |
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Selection |
Estimate selection for each codon using HyPhy, perform codon-based Z-test of selection, codon-based Fisher’s exact test of selection, or Tajima’s test of neutrality. |
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Rates |
Using Maximum Likelihood, estimate gamma shape parameter for site rates or estimate position-by-position rates. |
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Clocks |
Perform Tajima’s relative rate test, test for molecular clock, or compute a time tree using the Reltime Maximum Likelihood method. |
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Diagnose |
Explore the functional impact of non-synonymous single nucleotide variants (nSNVs). |
Secondary Toolbar
This toolbar contains items that are not suitable for the main toolbar.
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First time user? |
A very brief description of using MEGA. |
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Tutorial |
A collection of tutorials for learning how to perform common tasks when using MEGA. |
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Examples |
A collection of example data files that are used in the tutorials. |
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Citation |
How to cite MEGA. |
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Report a Bug |
Help improve MEGA by filing a bug report with the authors. |
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Updates? |
Check to see if there is a newer version of MEGA available. |
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MEGA Links |
Links to resources related to MEGA. |
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Toolbar |
Customize the main toolbar in MEGA. |
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Preferences |
Customize user preferences. |