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.
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.
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.
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.
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