Visual Tools for Data Management

5.6.1 Setup/Select Taxa & Groups Dialog

This dialog box has two sub-windows (Taxa/Groups and Ungrouped Taxa), a panel bar between them containing a few buttons, and a command panel, with the lower part containing the Add, Delete, Close, and Help buttons.

Taxa/Groups sub-window on the left: It shows all the currently defined taxa and group names hierarchically. If a taxon has been assigned to a group, it will appear connected to that group. Groups may be displayed in a collapsed format (indicated by a + mark before their name). You can click '+' to expand the group to a listing of the taxa

contained in it, and click ‘–‘ to collapse the group to only view the group name. Groups that do not contain any members do not have this box. Next is a checkbox indicating whether a given group or taxon will be included in an analysis. Following that is an icon indicating a taxon (single box) or a group (layer of boxes). Grayed out check boxes are used to indicate that some of the taxa in a group are selected and others are unselected. You can rearrange the order of taxa and groups using drag-and-drop. However, note that this order is not automatically used in the Data Explorer. To enforce this order, use the Sort command in the Data Explorer.

Ungrouped Taxa Sub-window on the right: This shows the names of all the taxa that do not belong to any of the groups to facilitate your ability to move taxa into groups. If this sub-window does not appear on your screen, then hold and drag the lower right corner of the dialog box to expand its width to unhide it.

Middle Command Panel: This resides between the above-mentioned two sub-windows and contains a splitter on its right edge. You can grab the splitter and move it to change the proportion of the space taken by the two sub-windows. In this panel left and right arrow buttons are used to add or remove taxa from the groups. Clicking the hand-with- a-pencil icon with a highlighted taxon or group name will allow you to edit that name. Lower Command Panel: In the lower part of the Select/Edit Taxa/Groups window are buttons that are used to add and/or delete groups. The ‘+’ and ‘–‘ buttons are also

present on the middle command panel.

Buttons Description

Add _{Creates a new group.}

Delete Deletes the currently selected group. Any taxa that were assigned to the group will become freestanding.

Ungroup Makes all the taxa in the selected group freestanding, but does not remove the group from the list.

Close _{Closes the dialog box.}

Help _{Brings up help regarding the dialog box.} How to perform functions:

Function Description

Creating a new group

Click on the Add button. Click on the highlighted name of the group and type in a new name.

Deleting a group Select the group and click the Delete button. Any taxa that were assigned to this group will become freestanding. Adding taxa to a

group

Drag-and-drop the taxon on the desired group or select one or more taxa in the Ungrouped Taxa window and click on the left arrow button on the middle command panel. Removing a taxon

from a group

Click on the taxon and drag-and-drop it into a group (or outside all groups). Or, select the taxon and click on the right arrow button on the middle command panel.

Include/Exclude taxa or groups

Click the checkbox next to the group or taxa name.

5.6.2 Groups of taxa

A group of taxa is a set of one or more taxa. Members of a group can be specified in the input data file, and created and edited in the Setup Taxa and Groups dialog.

Groups of taxa often are constructed based on their evolutionary relatedness. For example, sequences may be grouped based on the geographic origin of the source individual, or sequences from a multi-gene family may be arranged into groups consisting of orthologous sequences.

5.6.3 Data Subset Selection

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Any subset of sequence data can be selected for analysis using the options in the Data menu. You may:

1. Select Taxa (sequences) or Groups of taxa through the Setup/Select Taxa & Groups dialog box,

2. Choose Domains and Genes through the Setup/Select Genes & Domains dialog box,

Items 1 and 2 lead to the construction of a primary data subset, which is maintained until it is modified in the two dialog boxes mentioned in the above items or in the Sequence Data Explorer.

3. Select any combination of Codon Positions to use through the Analysis Preferences/Options dialog box from the Data | Select Preferences menu item in the main interface.

4. Choose to include only the Labeled Sites through the Data | Select Preferences menu item.

5. Decide to enforce Complete-Deletion or Pair-wise-Deletion of the missing data and alignment gaps.

Items 3, 4, and 5 provide the second level of data subset options. You are given relevant choices immediately prior to the start of the analysis. Therefore, these choices are secondary in nature and are specific to the currently requested analysis. The Analysis Preferences dialog box remembers them for your convenience and provides them as a default the next time you conduct an analysis that utilizes those options.

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You may select Select Taxa (sequences) or Groups of taxa through the Setup/Select Taxa & Groups dialog box to construct a distance matrix. You also can select

sequences in the Distance Data Explorer by clicking on the check marks next to the taxa names.

6 Part IV: Evolutionary Analysis