Distance Matrix Explorer

The Distance Matrix Explorer is used to display results from the pairwise distance calculations. It is an intelligent viewer with the flexibility of altering display modes and functionalities and for computing within groups, among groups, and overall averages.

This explorer consists of a number of regions as follows:

Menu Bar

File MenuHC_Dist_Matrix_Exp_File_Menu

Display MenuHC_Dist_Matrix_Exp_Display_Menu

Average MenuHC_Dist_Matrix_Exp_Average_Menu

Help: This button brings up the help file.

Tool Bar

The tool bar provides quick access to a number of menu items.

General Utilities

Lower-left Triangle button: Click this icon to display pairwise distances in the lower-left matrix. If standard errors (or other statistics) are shown, they will be displayed in the upper-right.

Upper-right Triangle button: Click this icon to display pairwise distances in the upper-right matrix. If standard errors (or other statistics) also are shown, they will be displayed in the lower-left.

(A, B): This button is an on-off switch to write or hide the name of the highlighted taxa pair. The taxa pair is displayed in the status bar below.

Distance Display Precision

$image\decimal_decrement.gif$ : This decreases the precision of the distance display by one decimal place with each click of the button.

$image\decimal_increment.gif$ : This increases the precision of the distance display by one decimal place with each click of the button.

Column Sizer: Has been replaced with an new system. Now simply move your mouse over the divider between the sequence name and the first column of data. Your cursor will change(to an arrow pointing left and right). Click and drag to resize the names.

Export Data

$image\seq_data_explorer_diskette.gif$ : This brings up the Exporting Sequence Data dialog box, which contains options to control how MEGA writes the output data, available options are Text, MEGA, CSV, and Excel.

The 2-Dimensional Data Grid

This grid displays the pairwise distances between taxa (or within groups etc.) in the form of a lower or upper triangular matrix. The taxa names are the row-headers; the column headers are numbered from 1 to m, with m being the number of taxa. There is a column sizer for the row-headers, so that you can increase or decrease the column size to accommodate the full name of the sequences or groups.

Fixed Row: This is the first row in the data grid and displays the column number.

Fixed Column: This is the first and leftmost column in the data grid. This column is always visible even if you scroll past the initial screen. It contains taxa names and an associated check box. To include or exclude taxa from analysis, you can check or uncheck this box. In this column, you can drag-and-drop taxa names to sort them.

Rest of the Grid: Cells to the right of the first column and below the first row contain the nucleotides or amino acids of the input data. Note that all cells are drawn in light color if they contain data corresponding to unselected sequences or genes and domains.

Status bar

The left sub-panel shows the name of the statistic for the currently selected value. In the next panel, the status bar shows the taxa-pair name for the selected value.