This menu provides commands for creating a new alignment, opening/closing sequence data files, saving alignment sessions to a file, exporting sequence data to a file, changing alignment sequence properties, reverse complementing sequences in the alignment, and exiting Alignment Explorer. The commands in this menu are:
Create New Alignment: This tells Alignment Explorer to prepare for a new alignment. Any sequence data currently loaded into Alignment Builder is discarded.
Open: This submenu provides two options: opening an existing sequence alignment session (previously saved from Alignment Explorer), and reading a text file containing sequences in one of many formats (including, MEGA, PAUP, FASTA, NBRF, etc.). Based on the option you choose, you will be prompted for the file name that you wish to read.
Reopen: Displays a list of recently opened files that can be activated in Alignment Explorer.
Close: This closes the currently active data in the Alignment Explorer.
Phylogenetic Analysis: Clicking this item will prepare the data in the active sequence alignment for further analysis in MEGA so that the alignment does not have to be saved to a file on disk and then reopened for analysis in MEGA.
Save Session: This allows you to save the current sequence alignment to an alignment session. You will be requested to give a file name to write the data to.
Export Alignment: This allows you to export the current sequence alignment to a file. There are three formats to choose from: MEGA, FASTA or PAUP/NEXUS formats. You will be requested to give a file name to write the data to.
DNA Sequences: Use this item to specify that the input data is DNA. If DNA is selected, then all sites are treated as nucleotides. The Translated Protein Sequences tab contains the protein sequences. If the data is non-coding, then ignore the second tab, as it has no affect on the on the DNA sequence tab. However, any changes you make in the Protein Sequence tab are applied to the DNA Sequences tab window. Note that you can UNDO these changes by using the undo button.
Protein Sequences: Use this item to specify that the input data is amino acid sequences. If selected, then all sites are treated as amino acid residues.
Translate/Untranslate: This item only will be available if protein-coding DNA sequences are available in the alignment grid. It will translate protein-coding DNA sequences into their respective amino acid sequences using the selected genetic code table.
Select Genetic Code Table: This displays the Select Genetic Code dialog window, which can select the genetic code table that is used when translating protein-coding DNA sequence data.
Reverse Complement: This becomes available when an entire sequence of row(s) is selected. It will update the selected rows to contain the reverse compliment of the originally selected sequence(s).
Exit AlnExplorer: This closes the Alignment Explorer window and returns to the main MEGA application window. When selected, a message box appears asking if you would like to save the current alignment session to a file. Then a second message box appears asking if you would like to save the current alignment to a MEGA file. If the current alignment is saved to a MEGA file, a third message box will appear asking if you would like to open the saved MEGA file in the main MEGA application.