TreeExplorer manual

[ Download TreeExplorer ]

It is strongly recommended to use the latest version integrated in MEGA3 available at http://www.megasoftware.net/. Thanks!

How to use TreeExplorer?

There are several ways to make an effect on a particular branch of tree, say, to place the root on the specified branch, as follows.

Click left mouse button to pick up the branch you want, and select the effect from the pull-down menu.
Click left mouse button to pick up the branch you want, and click the tool button.
Click left mouse button to pick up the branch you want, and select the effect from the popup menu showing up by right mouse button.
Select the function in the tool palette, and click left mouse button to specify the branch you want to make the effect.

Furthermore, there are several dialog boxes, in which you can set various parameters and attributes like tree size, line width, fonts, etc.

As a supporter of MEGA

There are two serious weak points in MEGA. One is that MEGA does not have a capability for saving tree data on disks and another is poor tree handling options and print quality. If you use TreeExplorer with MEGA, TreeExplorer can cover for these weak points by snatching tree that MEGA is displaying. Note that MEGA must be installed into the default folder, "C:\MEGA".

Notice for non-US version of Windows

We recently found that comma (,) is internally assigned to decimal point in some non-US version of Windows. Actually, many of European and South American countries are in this case. This causes a serious problem in TreeExplorer. Please use US-Windows or not use decimal point in the data file. If you use branch lengths with decimal point, please convert them to integer values by multiplying 100, 1000, etc.

Pull-down Menus and Tool Buttons

File

Open: [Ctrl-O]
Open a TreeExplorer-native binary file.

Import tree data:
TreeExplorer file:
Open a TreeExplorer-native text file.

Newick Standard file:
Open a Newick Standard format text file.

MEGA running:
Import a tree from MEGA running at the same time. This menu becomes active only when MEGA is running and showing a tree.

Save: [Ctrl-S]:
Save current tree into a TreeExplorer-native binary file.

Export tree data:
Current tree:
Save the tree showing on screen into a text file with TreeExplorer-native format.

All trees:
Save all the trees into a text file with TreeExplorer-native format.

Save as Windows EMF:
Save graphic image of current tree into a Windows Enhanced-Meta-File (EMF).

Print:
Print current tree as a fixed size. The size depends on the resolution of both of the screen and the printer you use. The number of pixels for printer is internally set to be four times as large as that for screen. Thus the tree size is exactly the same between the printout and the screen when the resolution of the printer is four times better than the screen, say, 400dpi printer versus 100dpi screen. If the tree size is bigger than the paper size, the tree is printed out on multiple sheets with a certain range of overlapping.

Print in a sheet: [Ctrl-P]:
Print current tree on a sheet of paper. This means that the tree is diminished to fit the paper size if it is too large.

Printer setup:
Setup printer options by simply calling Windows printer-setup dialog box.

Exit Tree Explorer: [Ctrl-Q]
Terminate the program.: Open a TreeExplorer-native binary file.
Import tree data:
TreeExplorer file:
Open a TreeExplorer-native text file.

Newick Standard file:
Open a Newick Standard format text file.

MEGA running:
Import a tree from MEGA running at the same time. This menu becomes active only when MEGA is running and showing a tree.

Save: [Ctrl-S]:
Save current tree into a TreeExplorer-native binary file.

Export tree data:
Current tree:
Save the tree showing on screen into a text file with TreeExplorer-native format.

All trees:
Save all the trees into a text file with TreeExplorer-native format.

Save as Windows EMF:
Save graphic image of current tree into a Windows Enhanced-Meta-File (EMF).

Print:
Print current tree as a fixed size. The size depends on the resolution of both of the screen and the printer you use. The number of pixels for printer is internally set to be four times as large as that for screen. Thus the tree size is exactly the same between the printout and the screen when the resolution of the printer is four times better than the screen, say, 400dpi printer versus 100dpi screen. If the tree size is bigger than the paper size, the tree is printed out on multiple sheets with a certain range of overlapping.

Print in a sheet: [Ctrl-P]:
Print current tree on a sheet of paper. This means that the tree is diminished to fit the paper size if it is too large.

Printer setup:
Setup printer options by simply calling Windows printer-setup dialog box.

Exit Tree Explorer: [Ctrl-Q]
Terminate the program.: TreeExplorer file:
Open a TreeExplorer-native text file.; Newick Standard file:
Open a Newick Standard format text file.; MEGA running:
Import a tree from MEGA running at the same time. This menu becomes active only when MEGA is running and showing a tree.
Save: [Ctrl-S]:
Save current tree into a TreeExplorer-native binary file.

Export tree data:
Current tree:
Save the tree showing on screen into a text file with TreeExplorer-native format.

All trees:
Save all the trees into a text file with TreeExplorer-native format.

Save as Windows EMF:
Save graphic image of current tree into a Windows Enhanced-Meta-File (EMF).

Print:
Print current tree as a fixed size. The size depends on the resolution of both of the screen and the printer you use. The number of pixels for printer is internally set to be four times as large as that for screen. Thus the tree size is exactly the same between the printout and the screen when the resolution of the printer is four times better than the screen, say, 400dpi printer versus 100dpi screen. If the tree size is bigger than the paper size, the tree is printed out on multiple sheets with a certain range of overlapping.

Print in a sheet: [Ctrl-P]:
Print current tree on a sheet of paper. This means that the tree is diminished to fit the paper size if it is too large.

Printer setup:
Setup printer options by simply calling Windows printer-setup dialog box.

Exit Tree Explorer: [Ctrl-Q]
Terminate the program.: Save current tree into a TreeExplorer-native binary file.
Export tree data:
Current tree:
Save the tree showing on screen into a text file with TreeExplorer-native format.

All trees:
Save all the trees into a text file with TreeExplorer-native format.

Save as Windows EMF:
Save graphic image of current tree into a Windows Enhanced-Meta-File (EMF).

Print:
Print current tree as a fixed size. The size depends on the resolution of both of the screen and the printer you use. The number of pixels for printer is internally set to be four times as large as that for screen. Thus the tree size is exactly the same between the printout and the screen when the resolution of the printer is four times better than the screen, say, 400dpi printer versus 100dpi screen. If the tree size is bigger than the paper size, the tree is printed out on multiple sheets with a certain range of overlapping.

Print in a sheet: [Ctrl-P]:
Print current tree on a sheet of paper. This means that the tree is diminished to fit the paper size if it is too large.

Printer setup:
Setup printer options by simply calling Windows printer-setup dialog box.

Exit Tree Explorer: [Ctrl-Q]
Terminate the program.: Current tree:
Save the tree showing on screen into a text file with TreeExplorer-native format.; All trees:
Save all the trees into a text file with TreeExplorer-native format.
Save as Windows EMF:
Save graphic image of current tree into a Windows Enhanced-Meta-File (EMF).

Print:
Print current tree as a fixed size. The size depends on the resolution of both of the screen and the printer you use. The number of pixels for printer is internally set to be four times as large as that for screen. Thus the tree size is exactly the same between the printout and the screen when the resolution of the printer is four times better than the screen, say, 400dpi printer versus 100dpi screen. If the tree size is bigger than the paper size, the tree is printed out on multiple sheets with a certain range of overlapping.

Print in a sheet: [Ctrl-P]:
Print current tree on a sheet of paper. This means that the tree is diminished to fit the paper size if it is too large.

Printer setup:
Setup printer options by simply calling Windows printer-setup dialog box.

Exit Tree Explorer: [Ctrl-Q]
Terminate the program.: Save graphic image of current tree into a Windows Enhanced-Meta-File (EMF).
Print:
Print current tree as a fixed size. The size depends on the resolution of both of the screen and the printer you use. The number of pixels for printer is internally set to be four times as large as that for screen. Thus the tree size is exactly the same between the printout and the screen when the resolution of the printer is four times better than the screen, say, 400dpi printer versus 100dpi screen. If the tree size is bigger than the paper size, the tree is printed out on multiple sheets with a certain range of overlapping.

Print in a sheet: [Ctrl-P]:
Print current tree on a sheet of paper. This means that the tree is diminished to fit the paper size if it is too large.

Printer setup:
Setup printer options by simply calling Windows printer-setup dialog box.

Exit Tree Explorer: [Ctrl-Q]
Terminate the program.: Print current tree as a fixed size. The size depends on the resolution of both of the screen and the printer you use. The number of pixels for printer is internally set to be four times as large as that for screen. Thus the tree size is exactly the same between the printout and the screen when the resolution of the printer is four times better than the screen, say, 400dpi printer versus 100dpi screen. If the tree size is bigger than the paper size, the tree is printed out on multiple sheets with a certain range of overlapping.
Print in a sheet: [Ctrl-P]:
Print current tree on a sheet of paper. This means that the tree is diminished to fit the paper size if it is too large.

Printer setup:
Setup printer options by simply calling Windows printer-setup dialog box.

Exit Tree Explorer: [Ctrl-Q]
Terminate the program.: Print current tree on a sheet of paper. This means that the tree is diminished to fit the paper size if it is too large.
Printer setup:
Setup printer options by simply calling Windows printer-setup dialog box.

Exit Tree Explorer: [Ctrl-Q]
Terminate the program.: Setup printer options by simply calling Windows printer-setup dialog box.
Exit Tree Explorer: [Ctrl-Q]
Terminate the program.: Terminate the program.

Edit

Swap subtrees:
Swap the position of two descendant subtrees of the focused branch.

Flip subtrees:
Flip the subtree under the focused branch so that in the subtree the OTU on the top goes to the bottom and the OTU at the bottom jumps up on the top.

Arrange taxa:
for Best tree shape:
Swapping and/or flipping subtrees automatically set the order of the OTUs for the best tree shape.

by input Order:
Swapping and/or flipping subtrees automatically set the order of the OTUs to follow the input order as much as possible.

Change Root:

on Focused Branch:
Place the arbitrary root on the focused branch for unrooted tree. When the root is already on a side of the focused branch, the root shifts onto the position specified by mouse clicking.

on Midpoint:
Place the arbitrary root on the midpoint of the longest path for unrooted tree.

by Outgroup:
Place the arbitrary root on a certain branch according to the pre-specified outgroup OTUs for unrooted tree.

Compress subtree:
Subtree under the focused branch is represented as an OTU.

Uncompress subtree:
Compressed subtree under the focused branch is recovered.

Uncompress All subtree:
All the compressed subtrees are recovered.

Set Divergence time:
Set divergence time for the focused node (far side of the focused branch from the root, usually right side), and thereby you can draw the time scale along the linearlized tree. When divergence time is known for neither of the nodes, yet you can enter evolutionary rate if available.

Display subtree:
Display subtree under the focused branch in a separate window.

Copy to clipboard: [Ctrl-C]
Copy the current tree image into the system clipboard so that other application programs can paste it if they have a capability to do so. Note that the image is not a mere bitmap but a set of draw objects and thus you can make additional effects at each branch or each OTU label level in draw software.: Swap the position of two descendant subtrees of the focused branch.
Flip subtrees:
Flip the subtree under the focused branch so that in the subtree the OTU on the top goes to the bottom and the OTU at the bottom jumps up on the top.

Arrange taxa:
for Best tree shape:
Swapping and/or flipping subtrees automatically set the order of the OTUs for the best tree shape.

by input Order:
Swapping and/or flipping subtrees automatically set the order of the OTUs to follow the input order as much as possible.

Change Root:

on Focused Branch:
Place the arbitrary root on the focused branch for unrooted tree. When the root is already on a side of the focused branch, the root shifts onto the position specified by mouse clicking.

on Midpoint:
Place the arbitrary root on the midpoint of the longest path for unrooted tree.

by Outgroup:
Place the arbitrary root on a certain branch according to the pre-specified outgroup OTUs for unrooted tree.

Compress subtree:
Subtree under the focused branch is represented as an OTU.

Uncompress subtree:
Compressed subtree under the focused branch is recovered.

Uncompress All subtree:
All the compressed subtrees are recovered.

Set Divergence time:
Set divergence time for the focused node (far side of the focused branch from the root, usually right side), and thereby you can draw the time scale along the linearlized tree. When divergence time is known for neither of the nodes, yet you can enter evolutionary rate if available.

Display subtree:
Display subtree under the focused branch in a separate window.

Copy to clipboard: [Ctrl-C]
Copy the current tree image into the system clipboard so that other application programs can paste it if they have a capability to do so. Note that the image is not a mere bitmap but a set of draw objects and thus you can make additional effects at each branch or each OTU label level in draw software.: Flip the subtree under the focused branch so that in the subtree the OTU on the top goes to the bottom and the OTU at the bottom jumps up on the top.
Arrange taxa:
for Best tree shape:
Swapping and/or flipping subtrees automatically set the order of the OTUs for the best tree shape.

by input Order:
Swapping and/or flipping subtrees automatically set the order of the OTUs to follow the input order as much as possible.

Change Root:

on Focused Branch:
Place the arbitrary root on the focused branch for unrooted tree. When the root is already on a side of the focused branch, the root shifts onto the position specified by mouse clicking.

on Midpoint:
Place the arbitrary root on the midpoint of the longest path for unrooted tree.

by Outgroup:
Place the arbitrary root on a certain branch according to the pre-specified outgroup OTUs for unrooted tree.

Compress subtree:
Subtree under the focused branch is represented as an OTU.

Uncompress subtree:
Compressed subtree under the focused branch is recovered.

Uncompress All subtree:
All the compressed subtrees are recovered.

Set Divergence time:
Set divergence time for the focused node (far side of the focused branch from the root, usually right side), and thereby you can draw the time scale along the linearlized tree. When divergence time is known for neither of the nodes, yet you can enter evolutionary rate if available.

Display subtree:
Display subtree under the focused branch in a separate window.

Copy to clipboard: [Ctrl-C]
Copy the current tree image into the system clipboard so that other application programs can paste it if they have a capability to do so. Note that the image is not a mere bitmap but a set of draw objects and thus you can make additional effects at each branch or each OTU label level in draw software.: for Best tree shape:
Swapping and/or flipping subtrees automatically set the order of the OTUs for the best tree shape.; by input Order:
Swapping and/or flipping subtrees automatically set the order of the OTUs to follow the input order as much as possible.
Change Root:

on Focused Branch:
Place the arbitrary root on the focused branch for unrooted tree. When the root is already on a side of the focused branch, the root shifts onto the position specified by mouse clicking.

on Midpoint:
Place the arbitrary root on the midpoint of the longest path for unrooted tree.

by Outgroup:
Place the arbitrary root on a certain branch according to the pre-specified outgroup OTUs for unrooted tree.

Compress subtree:
Subtree under the focused branch is represented as an OTU.

Uncompress subtree:
Compressed subtree under the focused branch is recovered.

Uncompress All subtree:
All the compressed subtrees are recovered.

Set Divergence time:
Set divergence time for the focused node (far side of the focused branch from the root, usually right side), and thereby you can draw the time scale along the linearlized tree. When divergence time is known for neither of the nodes, yet you can enter evolutionary rate if available.

Display subtree:
Display subtree under the focused branch in a separate window.

Copy to clipboard: [Ctrl-C]
Copy the current tree image into the system clipboard so that other application programs can paste it if they have a capability to do so. Note that the image is not a mere bitmap but a set of draw objects and thus you can make additional effects at each branch or each OTU label level in draw software.: on Focused Branch:
Place the arbitrary root on the focused branch for unrooted tree. When the root is already on a side of the focused branch, the root shifts onto the position specified by mouse clicking.; on Midpoint:
Place the arbitrary root on the midpoint of the longest path for unrooted tree.; by Outgroup:
Place the arbitrary root on a certain branch according to the pre-specified outgroup OTUs for unrooted tree.
Compress subtree:
Subtree under the focused branch is represented as an OTU.

Uncompress subtree:
Compressed subtree under the focused branch is recovered.

Uncompress All subtree:
All the compressed subtrees are recovered.

Set Divergence time:
Set divergence time for the focused node (far side of the focused branch from the root, usually right side), and thereby you can draw the time scale along the linearlized tree. When divergence time is known for neither of the nodes, yet you can enter evolutionary rate if available.

Display subtree:
Display subtree under the focused branch in a separate window.

Copy to clipboard: [Ctrl-C]
Copy the current tree image into the system clipboard so that other application programs can paste it if they have a capability to do so. Note that the image is not a mere bitmap but a set of draw objects and thus you can make additional effects at each branch or each OTU label level in draw software.: Subtree under the focused branch is represented as an OTU.
Uncompress subtree:
Compressed subtree under the focused branch is recovered.

Uncompress All subtree:
All the compressed subtrees are recovered.

Set Divergence time:
Set divergence time for the focused node (far side of the focused branch from the root, usually right side), and thereby you can draw the time scale along the linearlized tree. When divergence time is known for neither of the nodes, yet you can enter evolutionary rate if available.

Display subtree:
Display subtree under the focused branch in a separate window.

Copy to clipboard: [Ctrl-C]
Copy the current tree image into the system clipboard so that other application programs can paste it if they have a capability to do so. Note that the image is not a mere bitmap but a set of draw objects and thus you can make additional effects at each branch or each OTU label level in draw software.: Compressed subtree under the focused branch is recovered.
Uncompress All subtree:
All the compressed subtrees are recovered.

Set Divergence time:
Set divergence time for the focused node (far side of the focused branch from the root, usually right side), and thereby you can draw the time scale along the linearlized tree. When divergence time is known for neither of the nodes, yet you can enter evolutionary rate if available.

Display subtree:
Display subtree under the focused branch in a separate window.

Copy to clipboard: [Ctrl-C]
Copy the current tree image into the system clipboard so that other application programs can paste it if they have a capability to do so. Note that the image is not a mere bitmap but a set of draw objects and thus you can make additional effects at each branch or each OTU label level in draw software.: All the compressed subtrees are recovered.
Set Divergence time:
Set divergence time for the focused node (far side of the focused branch from the root, usually right side), and thereby you can draw the time scale along the linearlized tree. When divergence time is known for neither of the nodes, yet you can enter evolutionary rate if available.

Display subtree:
Display subtree under the focused branch in a separate window.

Copy to clipboard: [Ctrl-C]
Copy the current tree image into the system clipboard so that other application programs can paste it if they have a capability to do so. Note that the image is not a mere bitmap but a set of draw objects and thus you can make additional effects at each branch or each OTU label level in draw software.: Set divergence time for the focused node (far side of the focused branch from the root, usually right side), and thereby you can draw the time scale along the linearlized tree. When divergence time is known for neither of the nodes, yet you can enter evolutionary rate if available.
Display subtree:
Display subtree under the focused branch in a separate window.

Copy to clipboard: [Ctrl-C]
Copy the current tree image into the system clipboard so that other application programs can paste it if they have a capability to do so. Note that the image is not a mere bitmap but a set of draw objects and thus you can make additional effects at each branch or each OTU label level in draw software.: Display subtree under the focused branch in a separate window.
Copy to clipboard: [Ctrl-C]
Copy the current tree image into the system clipboard so that other application programs can paste it if they have a capability to do so. Note that the image is not a mere bitmap but a set of draw objects and thus you can make additional effects at each branch or each OTU label level in draw software.: Copy the current tree image into the system clipboard so that other application programs can paste it if they have a capability to do so. Note that the image is not a mere bitmap but a set of draw objects and thus you can make additional effects at each branch or each OTU label level in draw software.

Show

Rectangular branch:
Show tree in the rectangular branch style (example image).
Curved branch:
Show tree in the curved branch style (example image).
Linear branch:
Show tree in the linear branch style (example image).
Radiation tree:
Show tree in the radiation style. Available only for unrooted tree with branch length (example image).
Circle tree:
Show tree in the circular style. (example image).

Stats/Frequency:
Show or hide the statistics or frequencies for branches, say bootstrap values, along branches.
Branch Length:
Show or hide branch lengths along branches.

Taxon label:
Show or hide taxon labels.
Taxon Marker:
Show or hide taxon makers. Taxon marker is convenient to catch attention to a particular kind of OTUs or to reveal a classification of OTUs (example image). To setup the markers, use Format Dialog Box.

Scale Bar:
Show or hide scale bar.

Character state:
Unavailable in this version.

Information box: [Ctrl-I]:
Show or hide Information Dialog Box.

Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Show tree in the rectangular branch style (example image).
Curved branch:
Show tree in the curved branch style (example image).
Linear branch:
Show tree in the linear branch style (example image).
Radiation tree:
Show tree in the radiation style. Available only for unrooted tree with branch length (example image).
Circle tree:
Show tree in the circular style. (example image).

Stats/Frequency:
Show or hide the statistics or frequencies for branches, say bootstrap values, along branches.
Branch Length:
Show or hide branch lengths along branches.

Taxon label:
Show or hide taxon labels.
Taxon Marker:
Show or hide taxon makers. Taxon marker is convenient to catch attention to a particular kind of OTUs or to reveal a classification of OTUs (example image). To setup the markers, use Format Dialog Box.

Scale Bar:
Show or hide scale bar.

Character state:
Unavailable in this version.

Information box: [Ctrl-I]:
Show or hide Information Dialog Box.

Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Show tree in the curved branch style (example image).
Linear branch:
Show tree in the linear branch style (example image).
Radiation tree:
Show tree in the radiation style. Available only for unrooted tree with branch length (example image).
Circle tree:
Show tree in the circular style. (example image).

Stats/Frequency:
Show or hide the statistics or frequencies for branches, say bootstrap values, along branches.
Branch Length:
Show or hide branch lengths along branches.

Taxon label:
Show or hide taxon labels.
Taxon Marker:
Show or hide taxon makers. Taxon marker is convenient to catch attention to a particular kind of OTUs or to reveal a classification of OTUs (example image). To setup the markers, use Format Dialog Box.

Scale Bar:
Show or hide scale bar.

Character state:
Unavailable in this version.

Information box: [Ctrl-I]:
Show or hide Information Dialog Box.

Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Show tree in the linear branch style (example image).
Radiation tree:
Show tree in the radiation style. Available only for unrooted tree with branch length (example image).
Circle tree:
Show tree in the circular style. (example image).

Stats/Frequency:
Show or hide the statistics or frequencies for branches, say bootstrap values, along branches.
Branch Length:
Show or hide branch lengths along branches.

Taxon label:
Show or hide taxon labels.
Taxon Marker:
Show or hide taxon makers. Taxon marker is convenient to catch attention to a particular kind of OTUs or to reveal a classification of OTUs (example image). To setup the markers, use Format Dialog Box.

Scale Bar:
Show or hide scale bar.

Character state:
Unavailable in this version.

Information box: [Ctrl-I]:
Show or hide Information Dialog Box.

Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Show tree in the radiation style. Available only for unrooted tree with branch length (example image).
Circle tree:
Show tree in the circular style. (example image).

Stats/Frequency:
Show or hide the statistics or frequencies for branches, say bootstrap values, along branches.
Branch Length:
Show or hide branch lengths along branches.

Taxon label:
Show or hide taxon labels.
Taxon Marker:
Show or hide taxon makers. Taxon marker is convenient to catch attention to a particular kind of OTUs or to reveal a classification of OTUs (example image). To setup the markers, use Format Dialog Box.

Scale Bar:
Show or hide scale bar.

Character state:
Unavailable in this version.

Information box: [Ctrl-I]:
Show or hide Information Dialog Box.

Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Show tree in the circular style. (example image).
Stats/Frequency:
Show or hide the statistics or frequencies for branches, say bootstrap values, along branches.
Branch Length:
Show or hide branch lengths along branches.

Taxon label:
Show or hide taxon labels.
Taxon Marker:
Show or hide taxon makers. Taxon marker is convenient to catch attention to a particular kind of OTUs or to reveal a classification of OTUs (example image). To setup the markers, use Format Dialog Box.

Scale Bar:
Show or hide scale bar.

Character state:
Unavailable in this version.

Information box: [Ctrl-I]:
Show or hide Information Dialog Box.

Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Show or hide the statistics or frequencies for branches, say bootstrap values, along branches.
Branch Length:
Show or hide branch lengths along branches.

Taxon label:
Show or hide taxon labels.
Taxon Marker:
Show or hide taxon makers. Taxon marker is convenient to catch attention to a particular kind of OTUs or to reveal a classification of OTUs (example image). To setup the markers, use Format Dialog Box.

Scale Bar:
Show or hide scale bar.

Character state:
Unavailable in this version.

Information box: [Ctrl-I]:
Show or hide Information Dialog Box.

Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Show or hide branch lengths along branches.
Taxon label:
Show or hide taxon labels.
Taxon Marker:
Show or hide taxon makers. Taxon marker is convenient to catch attention to a particular kind of OTUs or to reveal a classification of OTUs (example image). To setup the markers, use Format Dialog Box.

Scale Bar:
Show or hide scale bar.

Character state:
Unavailable in this version.

Information box: [Ctrl-I]:
Show or hide Information Dialog Box.

Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Show or hide taxon labels.
Taxon Marker:
Show or hide taxon makers. Taxon marker is convenient to catch attention to a particular kind of OTUs or to reveal a classification of OTUs (example image). To setup the markers, use Format Dialog Box.

Scale Bar:
Show or hide scale bar.

Character state:
Unavailable in this version.

Information box: [Ctrl-I]:
Show or hide Information Dialog Box.

Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Show or hide taxon makers. Taxon marker is convenient to catch attention to a particular kind of OTUs or to reveal a classification of OTUs (example image). To setup the markers, use Format Dialog Box.
Scale Bar:
Show or hide scale bar.

Character state:
Unavailable in this version.

Information box: [Ctrl-I]:
Show or hide Information Dialog Box.

Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Show or hide scale bar.
Character state:
Unavailable in this version.

Information box: [Ctrl-I]:
Show or hide Information Dialog Box.

Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Unavailable in this version.
Information box: [Ctrl-I]:
Show or hide Information Dialog Box.

Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Show or hide Information Dialog Box.
Tool palette: [Ctrl-T]
Show or hide the tool button palette at the left side of the main window.: Show or hide the tool button palette at the left side of the main window.

Format

Tree Size:
Show Tree Size Dialog Box to set the size of tree and so forth.

Branch:
Show the branch page in Format Dialog Box.
Taxon name:
Show the taxon-name page in Format Dialog Box.
Scale bar:
Show the scale-bar page in Format Dialog Box.

Font:
Taxon Name:
Show the system font dialog box to set attributes of the font for taxon labels.

Subtree Name:
Show the system font dialog box to set attributes of the font for subtree labels.

Branch Information:
Show the system font dialog box to set attributes of the font for branch information like bootstrap values, branch lengths.

Scale Bar:
Show the system font dialog box to set attributes of the font for scale.

Character State:
Unavailable in this version.: Show Tree Size Dialog Box to set the size of tree and so forth.
Branch:
Show the branch page in Format Dialog Box.
Taxon name:
Show the taxon-name page in Format Dialog Box.
Scale bar:
Show the scale-bar page in Format Dialog Box.

Font:
Taxon Name:
Show the system font dialog box to set attributes of the font for taxon labels.

Subtree Name:
Show the system font dialog box to set attributes of the font for subtree labels.

Branch Information:
Show the system font dialog box to set attributes of the font for branch information like bootstrap values, branch lengths.

Scale Bar:
Show the system font dialog box to set attributes of the font for scale.

Character State:
Unavailable in this version.: Show the branch page in Format Dialog Box.
Taxon name:
Show the taxon-name page in Format Dialog Box.
Scale bar:
Show the scale-bar page in Format Dialog Box.

Font:
Taxon Name:
Show the system font dialog box to set attributes of the font for taxon labels.

Subtree Name:
Show the system font dialog box to set attributes of the font for subtree labels.

Branch Information:
Show the system font dialog box to set attributes of the font for branch information like bootstrap values, branch lengths.

Scale Bar:
Show the system font dialog box to set attributes of the font for scale.

Character State:
Unavailable in this version.: Show the taxon-name page in Format Dialog Box.
Scale bar:
Show the scale-bar page in Format Dialog Box.

Font:
Taxon Name:
Show the system font dialog box to set attributes of the font for taxon labels.

Subtree Name:
Show the system font dialog box to set attributes of the font for subtree labels.

Branch Information:
Show the system font dialog box to set attributes of the font for branch information like bootstrap values, branch lengths.

Scale Bar:
Show the system font dialog box to set attributes of the font for scale.

Character State:
Unavailable in this version.: Show the scale-bar page in Format Dialog Box.
Font:
Taxon Name:
Show the system font dialog box to set attributes of the font for taxon labels.

Subtree Name:
Show the system font dialog box to set attributes of the font for subtree labels.

Branch Information:
Show the system font dialog box to set attributes of the font for branch information like bootstrap values, branch lengths.

Scale Bar:
Show the system font dialog box to set attributes of the font for scale.

Character State:
Unavailable in this version.: Taxon Name:
Show the system font dialog box to set attributes of the font for taxon labels.; Subtree Name:
Show the system font dialog box to set attributes of the font for subtree labels.; Branch Information:
Show the system font dialog box to set attributes of the font for branch information like bootstrap values, branch lengths.; Scale Bar:
Show the system font dialog box to set attributes of the font for scale.; Character State:
Unavailable in this version.

Tool Palette

When any one of the tool buttons other than the point button, , is pick up by clicking moue without any focused branch, the mode of the mouse pointer is changed to have the function specified by the button. For example, after you select the "swap subtrees" function by clicking the corresponding button, , you can swap subtrees by one step, just clicking a branch you want to make the effect. It is extremely useful when you repeat the same action for many branches. The mode of the mouse pointer is reflected on the pointer icon (image).

Dialog Boxes

Tree Size Dialog Box:
Set entire size or unit size of tree (image). For circle tree, the start angle and the radius can be specified (image).
Format Dialog Box:
There are three pages in this dialog box.
Branch page:
Set the line width of branches, cut-off level for condensed or consensus tree, and show or hide and the position of bootstrap values and branch lengths, and more (image).

Taxon-Name page:
Set font attributes of taxon names and specify taxon marker icons (image).

Scale-Bar page:
Specify the length, tick interval and line width of scale bar, enter the unit name and setup its font attributes (image).
Information Dialog Box:
Unlike other dialog boxes, this dialog box just displays information about tree. There are three pages in this dialog box.
Method page:
Information about the tree making method is described in this page. (image)

Tree page:
Information about the tree is described in this page. (image)

Branch page:
Information about the focused branch is described in this page. (image)

Tree-Style Selection Box

TreeExplorer can display a phylogenetic tree in several different styles. The following tree styles can be selected in the "Tree-Style Selection Box".

Tree:
Ordinal phylogenetic tree with branches whose length is proportional to the real branch length. When there is no information about branch lengths, only the tree topology is displayed.
Topology:
Even when there is information about branch lengths, only the tree topology is displayed with branches whose length is arbitrary. This style is convenient when you want to pick up a very short branch. Note that this option is unavailable when there is no information about branch lengths. (image)
Condensed topology:
In this option, only the tree topology is displayed as well. However, the branches whose statistics value (e.g., bootstrap value) is lower than the specified value (in the branch page of Format Dialog Box) are set to have a branch lengths equal to 0. For details about the condensed tree, see the section 5.6.4 of MEGA manual. (image)
Linearlized tree:
The tree is converted to the linearlized tree according to Takezaki et al. (1995). In this style, scale bar for divergence times is available. Note that this option is available only when the distance data is supplied. (image)

Questions, Requests and Comments

Please mail to Dr. K. Tamura (koichiro-tamura@c.metro-u.ac.jp). Especially, bug reports will be greatly appreciated.