Tree viewer


You can see a phylogenetic tree of a division. There are two modes of the viewer, java mode (see 1.) and image mode (see 2.).

1. java mode

This is a default (and an initial) mode. In this mode, you can modify the view of the tree, and obtain a set of entries that belong to a specified node or OTU.
Functions or properties of parts of the viewer are described below.

1.1. menu bar

It locates on the top of the viewer. Items of the menu bar, which extracts a data set or changes drawing style of the map, are changed by the most left menu. The followings are functions of the items.

1.1.1. main menu

1.1.1.1. geometry

This is a sub-menu to change the geometry of the tree. You can change the style of the tree by selecting one of the sub-menu item after selecting a tree portion (see 1.2.1.).

1.1.1.2. zoom

This is a sub-menu to magnificate a portion of a tree. If you choose 'zoom up' after selecting a tree portion (see 1.2.1.), it is zoomed in. You have to notice that this is a simple magnification of a part of the tree, not a recalculation of a part of the tree. If you choose 'reset', the whole tree is displayed.

1.1.1.3. ID type

This is a sub-menu to choose a type of names to be displayed as OTU names. By default, 'accession' (accession number in DDBJ) is used.

1.1.1.4. redraw

You can force to redraw the graphic by clicking this button.

1.1.2. division menu

This menu is available on account mode only. You can make a private division from the obtained data. After selecting a tree portion and typing a division name in the field, the new private division is made by clicking 'make' button.

1.1.3. data menu

By clicking one of buttons in this menu after selecting a tree portion, the following data are obtained.

1.1.4. font menu

You can change a font (face, style, and size) which is used to draw OTU names and scales in the map.

1.1.5. scale menu

This menu controls the view of rulers. They are graduated in the number of substitution of bases (or residues) per site. After typing the scale span in a field in the menu, rulers are displayed by choosing one of the following sub-menu items.

1.1.6. bootstrap value menu

This menu is available on divisions to which boostrap anayses have been done. After typing the minimum number of bootstrap value in a field in the menu, the values are displayed by choosing by choosing one of the following sub-menu items. The values equal or over the specified minimum value are drawn near the corresponding nodes.

1.2. tree graphic

At the center of the viewer, a phylogenetic tree of a division is displayed.

1.2.1. To choose a portin of a tree

You may choose a part of a drawn tree to change its drawing style or to obtain the corresponding data set. If you click one of the nodes (OTUs or branching points), the node and its downstream are drawn in red, which shows that the portion is selected. You can do so by choose a proper menu item after that.

1.3. items to change the graphic size

You can change the size of graphic by typing width/height to fields and then clicking 'resize' button.

1.4. links to the other data types

At the bottom of the viewer, links to the other data types of the division are prepared as follow.

2. image mode

In this mode, map is displayed by a JPEG image file instead of JAVA. Although tree style modification or data set extraction is not available in the mode, you can print or save the tree graphic. You can use the mode of the viewer by clicking '[image mode]' at the bottom of the java-mode viewer.
Functions or properties of parts of the viewer are described below.

2.1. map graphic

At the top of the viewer, a map is displayed by nearly the same style as java-mode map. If you click one of the OTU names, the annotation of the entry is displayed.

2.2. items to change the graphic style

You can change the style of the graphics. Options are as follow. After setting the above option, you can get a new tree graphic by clicking 'redraw' button.

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