TreeView Help: File formats

Contents
Saving trees
Clustal W
COMPONENT
Hennig86
MacClade
PAUP
PAUP*
PHYLIP
Ribosomal Database Project

Saving trees to different file formats

TREEVIEW can save trees to different file formats, but does not ensure that the labels are consistent with that program. For example, PHYLIP requires labels of only 10 characters in length, whereas other programs may have much longer taxon names. If you anticipate moving trees between programs you will need to ensure that the labels you use will be acceptable to all the programs.

ClustalW

ClustalW produces .DND and .PHB files which TREEVIEW can read. The bootstrap values in .PHB trees are stored as labels for the internal nodes. These can be viewed using the Show Internal Labels command.

COMPONENT

TreeView will read COMPONENT tree files, but not files with DISTRIBUTION blocks.

Hennig86

Hennig86 tree files do not have taxon names, so the taxa from a Hennig86 file will be labelled "0", "1", etc. Likewise, when trees are saved in this format any taxon names will be lost.

MacClade

TreeView reads NEXUS tree files and so will accept MacClade tree files (but not data files). However, it will not cope with trees of different sizes in the same file (for example, if you've deleted branches from some but not all the trees).

PAUP

TreeView will not read data files, but should accept all PAUP tree files with fewer than 200 terminal taxa.

PAUP* for DOS and Unix

The forthcoming PAUP* will be available on DOS and Unix machines as a command line program. If you run the DOS version under Windows you can readily view tree files produced by the PAUP* command SAVETREES, either by opening the files in TREEVIEW, or by using drag and drop. To do the later, open File Manager to view the directory to which you are writing your tree files. To view a file, simply drag it onto the TREEVIEW application.

To view trees produced by the Unix version you will need to ftp them to your Mac or PC.

Note that to get branch lengths from the command line versions you need to specify the BRLENS option, e.g.

SAVETREES /BRLENS=YES;

PHYLIP

PHYLIP CONSENSE, rather unfortunately, outputs the frequency of each node in the input trees (the profile) as the length of the corresponding edge. To view these values use the Show Internal Labels command.

Ribosomal Database Project (RDP)

The RDP (http://rdp.life.uiuc.edu/) allows phylogenetic analysis over the Internet. You can submit a sequence and receive a tree back by email in Newick format (see http://rdp.life.uiuc.edu/RDP/commands/sgtree.html for details). This tree is readable by TREEVIEW. Simply cut and paste the tree description into a text file, save the file, then open it in TREEVIEW. Note that the tree is preceded by a header that looks like this:

%----------------------------------------------------------------------

              RDP Mail Server Revision 5.0 18-MAY-1995
           If you have problems or questions about the server
              send email to  rdp@phylo.life.uiuc.edu

%----------------------------------------------------------------------
Do not include this header in the file to be viewed by TREEVIEW.

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