TreeView Help: Frequently asked questions

Some frequently asked questions about TreeView.

Contents
Why won't TreeView for Windows start?
Why won't TreeView display bootstrap values for ClustalX trees?
How can I display bootstrap values from PAUP*?
Why doesn't the tree editor save my changes to the tree?
Is TreeView Year 2000 (Y2K) compliant?
Why doesn't the tree editor save my changes to the tree?
My tree pictures are clipped in Microsoft Word

Why won't TreeView for Windows start?

The Windows version of TreeView may crash on startup for no apparent reason (you may encounter this problem if you have a new PC or have upgraded to a more recent version of Windows). This is because when it starts up TreeView reads gets information about your default printer. If you don't have a default printer driver installed the program crashes. To fix this, simply install a printer driver. You don't actually need a printer attached to your PC, just a printer driver.

Why won't TreeView display bootstrap values for ClustalX trees?

The online documentation for ClustalX states:

  "By default, the bootstrap values are correctly placed on the tree branches of the phylip format output tree. The toggle allows them to be placed on the nodes, which is incorrect, but some display packages (e.g. TreeTool, TreeView and Phylowin) only support node labelling but not branch labelling. Care should be taken to note which branches and labels go together." [my emphasis]  

In fact there is little consensus about where in a tree description one should place bootstrap values, and hence different programs support different solutions, such as replacing branch lengths with bootstrap values (PHYLIP, optional in PAUP*), using node labels (TreeView, ClustalW, optional in PAUP* and ClustalX), placing them inside brackets "[ ]" after the branch lengths (ClustalX default), and so on. In the absence of a standard, TreeView uses node labels. It will ignore labels inside "[ ]" as any such text is treated as a comment.

If you are using ClustalX you can tell the program to output bootstrap values as node labels using the Output Format Options command on the Trees menu. In the dialog box select NODE in the Bootstrap labels on popup menu.

How can I display bootstrap values from PAUP*?

You can save bootstrap values computed using PAUP* in a form TreeView will read. Once you've done a bootstrap analysis, save the trees to a file. On a Mac use the Save Trees command. In the Save Trees dialog box click on the Options button.

You need to tell PAUP to set the maximum decimals to 0, and to include bootstrap values in the file as internal node labels. The equivalent command line for Windows/Unix users is

savetree SaveBootP=NodeLabels MaxDecimals=0; 

Open the tree in TreeView and select Show Internal Edge Labels from the Trees menu.

 

Why doesn't the tree editor save my changes to the tree?

The tree editor only saves "non-cosmetic" changes to the tree, such as moved branches or collaped clades. Other changes, such as rotating nodes, do not change relationships among the taxa and hence are not saved. This is because the editor was designed to enable the user to create new tree topologies, not to improve the appearance of a tree for printing.

If you change the topology of the tree then when you close the editor it will ask you whether you want to save the changes to the tree. The edited tree will then be displayed in the original tree window.

Is TreeView Year 2000 (Y2K) compliant?

TreeView does not perform any operations on dates and so should perform normally during or after January 1, 2000. Please note that this information is provided as a courtesy and should not be considered a certificate, guarantee, or warranty. Remember that TreeView is provided "as is" and the following statement (from the TreeView manual) applies:

THE SOFTWARE IS PROVIDED "AS-IS" AND WITHOUT WARRANTY OF ANY KIND, EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.IN NO EVENT SHALL THE AUTHOR, THE DIVISION OF ENVIRONMENAL AND EVOLUTIONARY BIOLOGY OR THE UNIVERSITY OF GLASGOW BE LIABLE FOR ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

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