General information

When the ‘Draw phylogenetic tree’ option is chosen from the main menu, an evolutionary tree can be drawn on the screen.  Initially, trees are drawn in their optimal form, which means that the length of the vertical branches is minimized, in order to optimize visual interpretation.  Trees can be scrolled in both directions and customized to the needs of the user.  However, keep in mind that an evolutionary tree has to be computed before it can be drawn on the screen, unless you want to redraw a tree that has been saved in the TREECON or bracket format (see further).  The option ‘scale’ can be used to enlarge or to reduce the tree.  To add bootstrap values, or a distance scale, choose the ‘show’ option.  Changing fonts for these items afterwards should be done by selecting the option ‘customize’.  A list of fonts is provided by MS-Windows itself, and all these can be used to draw the species (sequence) names, bootstrap values and so on.  Groups of sequences can be represented as a triangle, taxon designations can be added and a group of sequences can be selected by coloring the background enclosing this group.  It is also possible to select a group of sequences and draw them in a different font.  Furthermore, branches can be swapped and the trees can be rooted at alternative places.

Although most options in the DRAW program are self-explanatory, an overview is given of most of the different options available in the TREECON drawing program.

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Drawing a newly constructed tree

When a new tree has just been computed, it can be shown on the screen by choosing the option File|Open|(new)tree or by pressing the toolbar button that says ‘Load new tree’.

Trees saved in the TREECON format

When trees have been saved in the TREECON format, they can be reopened any time by selecting File|Open|tree in TREECON format or by pressing the toolbar button that says ‘Load tree in TREECON format’.  The default extension of trees saved in the TREECON format is ‘.trc’.  See Saving trees in the TREECON format for a discussion of the TREECON format into more detail.

The New Hampshire bracket format is a standard of writing and saving trees that has been adopted on June  24, 1986 at the annual meetings of the Society for the Study of Evolution at a meeting (the final session in Newick's lobster restaurant  --  hence  its name  --  the  Newick  standard) of an informal committee consisting of Wayne Maddison (developer of  MacClade), David Swofford (developer of PAUP), F. James Rohlf  (developer of NTSYS-PC),  Chris Meacham  (developer of COMPROB  and plotting  programs),  James Archie  (developer of the character  coding program), William H.E. Day, and Joe Felsenstein.   The standard is a generalization of PHYLIP's format.  Besides the classical bracket format as used by PHYLIP and other tree inferring programs, TREECON can also read the bracket format used by James S. Farris in his Hennig86 and Parsimony Jackknifer programs (Farris et al., 1996).  This ‘bracket’ format is slightly different because it supports multifurcations.  James S.  Farris is greatly acknowledged for sharing his code to convert this format into a format that’s suitable for TREECON.  In fact, all code to read bracket formats was based on the code supplied by James S. Farris.  It should be noted that, for (most) bootstrapped trees saved in the New Hampshire format, the branch lengths are meaningless. At the moment, it is not yet possible to save TREECON trees in the bracket format.

Since there are some differences in the bracket formats saved by the different software programs, two options are available in TREECON to read trees saved in the bracket format.  The first option (File|Open|tree in New Hampshire bracket format) reads the following formats:
 

• non-bootstrapped trees saved by PHYLIP
• bootstrapped trees saved by PHYLIP
• trees saved by Parsimony Jackknifer
• non-bootstrapped trees saved by CLUSTAL

The second option (File|Open|tree in New Hampshire bracket format (optional)) reads the following formats:
 

• bootstrapped trees saved by CLUSTAL
• trees saved by PUZZLE

Examples

SAVING AND COPYING TREES

Saving trees in the TREECON format

Trees that have been constructed by TREECON are best saved in the TREECON format (File|Save tree|as TREECON file or toolbar button that says ‘Save tree in TREECON format’).   The major advantage of saving trees in this format is that customizations are saved and that the trees can be retrieved and changed at any time.  This option is very interesting to store all your trees, in case you need them later.

The only thing that is not saved (yet) are swapped branches

Trees can also be saved in the Hewlett Packard Graphical Format (HPGL) (File|Save tree|as HPGL file.  This format, which is a very simple one and widely distributed, has the advantage that it can be edited by graphical programs, such as DrawPerfect, WordPerfect Presentations or CorelDraw. However, some options such as the representation of clusters as isosceles triangles, or the addition of taxon designations, are not saved in the HPGL format.  It is also possible that the bootstrap values are not placed perfectly on the tree saved in the HPGL format.  However, by selecting them all together in the drawing program, they can easily be dragged to their final destination.

More interesting though is to copy the tree to the clipboard (see further) and paste it into a drawing program such as MS-Powerpoint or CorelDraw

A third option is to save the tree as a DOS text file.  This option should be chosen if trees are saved containing hundreds of sequences, since the DRAW program is primarily developed for the drawing of small publishable trees (up to 100 or so sequences). Trees saved by this option have a somewhat lower resolution but can be edited by word-processing software.  If you want to save the tree as a text file, don’t bother about fonts or customizations.  Options such as the representation of clusters as isosceles triangles, or the addition of taxon designations, are not saved in the text format.

If you need to save the tree as a postscript file, install a postscript printer (add a postscript driver) in Windows (e.g. Apple laserwriter).  When selecting a postscript printer you usually have the choice to send the tree directly to the printer or to send the tree to a file (see Printer options).  If you send it to a file, a postscript file is created that contains the tree as it appeared on the screen (WYSIWYG). You can then print this postscript file on a postscript printer whenever you like.  When a postscript printer is not available, software exists (e.g. GoScript) to print postscript files on non-postscript printers.

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One of the most interesting new features in the TREECON drawing program is the possibility to copy and paste trees.  When the option File|Copy is selected (or by pressing the toolbar button that says ‘Copy (to clipboard)’), trees are copied to the clipboard and can be pasted to other Windows programs.  For example, if you would like to make slides of the trees constructed with TREECON, copy the tree, and paste it into a program such as MS-Powerpoint or Aldus Persuasion.  By ‘ungrouping’ the trees, the different objects of the tree (branches, names, bootstrap values, etc…) can be edited and changed to the needs of the user.

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Groups of sequences can be represented in different ways. Where possible, a point-and-click approach is implemented to make the selection of a group of sequences as easy as possible.

The first possibility to select a group of sequences is by putting them in a different font.  This can be done by choosing the option Select|Select (group of) sequence(s).  A list of sequences is then displayed and the user can make a selection.  Afterward, another font (or colour) can be chosen for the selected sequences.  Five groups of sequences can be selected this way.

A monophyletic group of sequences can also be represented as an isosceles triangle.  E.g. when the option Select|Select monophyletic cluster as triangle (or toolbar button ‘Represent cluster as triangle’)  is chosen from the menu, squares are drawn on the branching points of the tree. By pointing the mouse on such a square and clicking, a group of sequences descending from that particular branch is selected and represented as a triangle.  The height of the triangle is equal to the mean distance separating the sequences forming the cluster from the deepest branching point within that cluster, while the base is proportional to the number of sequences.  Triangles can be put in different colours and the name can be given to the cluster represented by the triangle.  To delete a triangle, choose the option Select|Deselect cluster as triangle.  At the moment, twenty triangles can be selected.

It is also possible to select a monophyletic group of sequences by changing the background colour enclosing this group (Select|Select monophyletic cluster by shading or toolbar button ‘Shades a cluster’).  Different colors can be chosen for the shading and the right border of the shading can be moved (see customizing a tree).

Taxon designations can be added for monophyletic as well as for paraphyletic groups of sequences.  When the option Tools|Add taxon designation (or toolbar button ‘Add (monophyletic/paraphyletic) taxon designation’) is chosen from the menu, squares are drawn on the branching points of the tree. By pointing the mouse on such a square and clicking, a taxon designation for the group of sequences descending from that particular branch can be defined.  The program asks for the name of the taxon, and then a border delimiting the taxon is drawn.  The taxon border style and the thickness of the taxon border can be changed (under customization).  It is also possible to add a taxon designation for a single sequence, by selecting the endnode leading to this sequence.  The orientation of the taxon names can be changed and a different font can be selected for the taxon names (see customization).  Deleting taxon designations can be done with the option Tools|Delete taxon designation.

When a taxon designation is wanted for a paraphyletic group of species, it is necessary to select two sequences, namely the one forming the upper bound of the taxon designation, and the one forming the lower bound.

BOOTSTRAP VALUES

When bootstrap analysis has been performed, bootstrap values can be displayed on the tree (Show|Bootstrap values or toolbar button ‘Add bootstrap values’).  Bootstrap values at a branching point denote the number of bootstrap trees comprising a cluster of the same composition.  In TREECON, you can select the bootstrap percentage above which the bootstrap values have to be displayed.  Furthermore, you can decide whether branches showing a lower percentage should be drawn as resolved or as unresolved.  When branches are drawn as unresolved, branch lengths are reduced to 0 which gives a multifurcating branching pattern.  However, since some branch lengths are reduced to 0, the evolutionary distance between some sequences may be slightly underestimated.  Nevertheless, the tree drawn is the best approximation of the original tree.  If bootstrap values overlap each other, try to rearrange the branching order with the option Topology|Swap branches, or by choosing a smaller font for the bootstrap values.

If you want to print a tree with bootstrap values, change the background colour to white

REROOTING A TREE

In the draw program, non-bootstrapped trees can be rerooted at any time.  The tree can be rerooted with a single sequence (Topology|Change root|Root with single sequence), or it can be rooted by selecting a group of sequences (Topology|Change root|Root at internode).

As already stated, caution should be taken when rerooting bootstrapped trees.  Here’s how to proceed.
First, draw the newly constructed tree and select the option 'Show|Bootstrap values'.  Then reroot the tree (always after the bootstrap values have been displayed on the tree).  If you have made a mistake and selected the wrong (multiple) outgroup, always reroot with the original one-species outgroup first before rerooting at an internode again.  In TREECON for Windows this is very easy.  Select Topology|Change root|Root with single sequence, and select the sequence initially used to root the bootstrap trees.

SCALING A TREE

The option Scale can be used to enlarge or reduce the tree.   Toolbar buttons (‘Increase/Decrease the ordinate’ and ‘Increase/Decrease the abscissa’) are also available for decreasing and increasing the width and length of the tree.

CHOOSING A PAPER FORMAT

When the draw program is started, the page boundaries corresponding with a portrait A4 paper format are shown in dotted lines.  When the tree is scaled within these boundaries, it will be printed completely on an A4 paper format.  However, several other paper formats can be chosen (Select File|Paper format).  Mind though that you should also change printer settings correspondingly.

ADDING A DISTANCE SCALE

A distance scale, representing the evolutionary distance,  can be displayed on top of the evolutionary tree.  Different titles can be chosen or a new title can be added.  The scale itself represents 0.10, 0.05, or 0.02 fixed mutations per site.  To put a scale on the tree, choose Show|Distance scale from the menu.  Different fonts for the title can be selected under Customize|Distance scale|Font.

The evolutionary distance between two organisms or groups of organisms is obtained by summing the lengths of the connecting branches along the horizontal axis, using the scale on top.

For trees constructed by clustering, the distance between two sequences or groups of sequences can be derived directly from the scale on top, since all branches end at the same point (so lengths of the connecting branches along the horizontal axis do not have to be summed up).

CUSTOMIZING A TREE

Under Customize, different fonts can be selected for sequence names, bootstrap values, taxon designations, cluster names, ….  When the Customize|Font option is selected, windows gives a list of available fonts the user can choose from.

Different colours can be selected for triangles, for shading groups of sequences, and for the background.  When the option Customize|Colour  is chosen, the colour palette of Windows is shown, and a specific colour can be selected.
Under Customize, the names of sequences, triangles, and taxon designations can be changed.

Furthermore, also the position of the taxon designations and the right borders of the shaded backgrounds can be changed.

DRAWING UNROOTED TREES

If an outgroup is not available to root the tree, unrooted tree topologies can be drawn (for small trees).  Of course, also rooted tree topologies can be displayed as if they are unrooted.

When a tree is drawn as unrooted, this does not mean that the 'root unrooted tree' option of TREECON should be skipped. Trees constructed with neighbor-joining should always be rooted before they are being displayed in the drawing program.  However, when one wants to draw the tree as unrooted afterwards, selection of the rooting sequence is of no importance.

Several options are available to draw the unrooted tree in its optimal form.

When the tree is first drawn as unrooted, it is possible that part of the tree is not visible.  This can be solved by moving the tree by selecting Topology|Move tree or by pressing the toolbar button that says ‘Move tree’.   Then push the left mouse button and drag.  When the left mouse button is released, the tree will move over the distance selected by the dragging.  If the tree has been moved to its final destination, push the cancel button.

The unrooted tree can be rotated to the left or to the right.  Select Topology|Rotate tree or press the toolbar buttons that say ‘Rotate left’ or ‘Rotate right’.  Rotating the tree should be done before dragging (changing the arcs of ) individual branches (see further).

When a tree is first drawn as unrooted, branches are spread over 360 degrees.  It is possible to change the angle of the arc of the total tree.  Sometimes, this gives very nice results (it depends on the number of sequences).  Changing the angle of the arc of the tree can be done by selecting Topology|Changing angle or by pressing the toolbar button that says ‘Arc of tree’.  Defining the angle of the arc of the tree should also be done before dragging (changing the arcs of ) individual branches (see further).

After the tree has been rotated (if needed) the orientation of individual branches can be changed by dragging.  Select Topology|Drag branches or press the toolbar that says ‘Drag branches’.  Squares are drawn on the internodes and endnodes of the tree and by pushing the left mouse button on such a square and dragging, the orientation of a branch or a cluster of branches - indicated in blue - can be changed.

The unrooted tree can be enlarged or reduced by selecting the Zoom option or by pressing the toolbar buttons that say ‘Zoom in’ and ‘Zoom out’.