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.).
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.).
- set root
The geometry is changed so that all the entries downstream the selected nodes
consist one cluster and the rest entries consist another cluster.
- exchange
Two branches of the selected node are exchanged each other.
- reset
Reset to the initial geometry.
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.
- entry : full annotated data (entries)
- sequence : nucleic acids sequences
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.
- none : A ruler is disappeared.
- upper : A ruler is drawn at the upper side of the tree.
- lower : A ruler is drawn at the lower side of the tree.
- both : Rulers are drawn at the both sides of the tree.
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.
- none : Bootstrap values are disappeared.
- show : Bootstrap values are drawn.
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.
- [alignment] : multiple alignment
- [matrix] : genetic distance matrix
- [sequence] : nucleic or amino acids sequences
- [entry] : full annotated data
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.
- image size : type width and height in the fields
- font size : choose a font size from the menu
- distance scale : controls to display rulers by the same manner as
java-mode viewer (see 1.1.5.)
- OTU name tag : controls the type of drawn names used as OTU names by the
same manner as java-mode viewer (see 1.1.1.3.)
- min bootstrap : type minimun boostraping value, which is used as the
same manner as java-mode viewer (see 1.1.6.)
After setting the above option, you can get a new tree graphic by clicking
'redraw' button.