Thank you for choosing to use MEGA in your research. You may wish to read and follow along with our walkthrough tutorial. The walkthrough attempts to touch on every major part of MEGA which you may find useful.
Quick Start (useful for more technical users)
Running an Analysis
(Note: Sequences MUST be aligned before analysis can proceed.)
Select the analysis you wish to run from the menu on the main window.
You are shown a list of options for this analysis. You can only change the options which are highlighted in Yellow. Click Compute.
Depending on the length of the analysis you may see a progress bar while the analysis is running.
Your output will appear as either a Tree, Matrix, Text, etc.
In most results there will be the option to save your analysis. This usually resides in the File or Data menus of the results window.
Aligning Sequences
MEGA supports sequence alignment using both the ClustalW and MUSCLE programs.
Alignment (or refinement) is done in the Analysis Explorer (Alignment -> Open Alignment Explorer from main menu).
We either can start with a blank alignment (if we are importing sequences from NCBI, or dont have a compatible sequence file) or from a compatible sequence file.
With our sequences in the Alignment Explorer (AE), we select Alignment from the menu, then either ClustalW or Muscle.
Set the alignment parameters to the values you wish or leave the options alone to use the defaults. Click Compute/OK.
Depending on the length and number of sequences you may see a progress bar while the alignment is running.
The aligned sequences will replace the previously unaligned sequences in the Alignment Explorer. You may now export them to MEGA or Fasta format for analysis.