A Short Introduction
To use DRAWTREE and DRAWGRAM, you must have
- The compiled version of the program. If you have not obtained a version of PHYLIP precompiled for your machine, you will have to take the source code given here and modify it for your C compiler and then compile it. This is not too hard: it is discussed below.
- A tree file. Trees are described in the nested-parenthesis notation used throughout PHYLIP and standardized in an informal meeting of program authors in Durham, New Hampshire in June, 1986. Trees for both programs may be either bifurcating or multifurcating, and may either have or not have branch lengths. Tree files produced by the PHYLIP programs are in this form.
- A font file. There are six font files distributed with PHYLIP: these consist of three Roman, two Italic, and one Russian Cyrillic font, all from the public-domain Hershey Fonts, in ASCII readable form. The details of font representation need not concern you; all you need to do is to copy the font file corresponding to the font you want into the appropriate directory under the appropriate file name, and let the program use it. Or you can let the program ask you for the name of the font file, which it will do if it does not find one itself. The six fonts are, respectively, a one- and a two-stroke sans-serif Roman font, a three-stroke serifed Roman font, a two- and a three- stroke serifed Italic font, and a two-stroke Cyrillic font for the Russian language. If this is not clear just try them all. Note that for Apple Laserwriters (or other Postscript printers) several built-in fonts can be used too.
- A plotting device, and if possible a screen on which you can preview the plot. The programs work with Postscript-compatible laser printers, laser printers compatible with the Hewlett-Packard Laserjet series, plotters including Hewlett-Packard models, dot matrix printers including models by Epson and Apple, graphics terminals from DEC and Tektronix, IBM PC graphics screens, the PCX file format for the PC Paintbrush painting program, the PICT format for the MacDraw drawing program, the file format for the public domain X-windows drawing program "xfig", the X Bitmap format for X-windows, and, strangest and most wonderful of all, the input format for the public-domain ray-tracing (3- dimensional rendering) program "rayshade". You choose the plotting and previewing devices from a menu at run time, and these can be different. There are places in the source code for the program where you can insert code for a new plotter, should you want to do that.
Once you have all these the programs should be fairly self explanatory, particular if you can preview your plots so that you can discover the meaning of the different options by trying them out.
Once you have a compiled version of the appropriate program, say DRAWGRAM, and a file called (say) TREEFILE with the tree in it, and a font file (say FONT2 which you have copied as a file called FONTFILE), all you do is run the program DRAWGRAM. It should automatically read the font and tree files, and will ask you to choose the graphics devices. Then it will let you see the options it has chosen, and ask you if you want to change these. Once you have modified those that you want to, you can tell it to accept those. The program will then allow you to preview the tree on your screen, if you have told it that you have an appropriate graphics screen (the PCDOS and 386 PCDOS versions of the program will automatically adapt to a number of the commonest PC graphics boards, and the Macintosh version will adapt to the Macintosh screen). After previewing the tree, it will ask if you are ready to plot the tree. If you say no, it will once again allow you to change options and will the allow you to preview the tree again, and so on as many times as you want. If you say yes, then it will write a file called (say) PLOTFILE. If this file is copied directly to your plotter or printer, it should result in a beautifully plotted tree. If the final plotting device is a DEC or PCDOS graphics screen, it may not write a plot file but will plot directly on the screen.
Having read the above, you may be ready to run the program. Below you Will find more information about representation of trees in the tree file, on the different kinds of graphics devices supported by this program, and on how to recompile these programs. If you have (for example) a PCDOS system and a compiled version of the program, then all you have to do is have a tree file called TREEFILE, a font file called FONTFILE, and run the program. Then copy PLOTFILE to your plotter or printer.
The New Hampshire Standard for representing trees in computer-readable
form makes use of the correspondence between trees and nested parentheses,
noticed in 1857 by the famous English mathematician Arthur Cayley. If we have
this rooted tree:
Tips are represented by their names. A name can be any string of
printable characters except blanks, colons, semcolons, parentheses, and square
brackets. In the programs a maximum of 30 characters are allowed for names:
this limit can easily be increased by recompiling the program and changing the
constant declaration for "nch" at the beginning of the program.
Because you may want to include a blank in a name, it is assumed that an
underscore character ("_") stands for a blank; any of these in a name will be
converted to a blank when it is read in. Any name may also be empty: a tree
like
Branch lengths can be incorporated into a tree by putting a real number,
with or without decimal point, after a node and preceded by a comma. This
represents the length of the branch immediately below that node. Thus the
above tree might have lengths represented as:
The tree starts on the first line of the file, and can continue to
subsequent lines. It is best to proceed to a new line, if at all, immediately
after a comma. Blanks can be inserted at any point except in the middle of a
species name or a branch length.
The above description is of a subset of the New Hampshire Standard. For
example, interior nodes can have names in that standard, but if any are
included the present programs will omit them.
To help you understand this tree representation, here are some trees in
the above form:
The New Hampshire Standard was adopted June 26, 1986 by an informal
committee meeting during the Society for the Study of Evolution meetings in
Durham, New Hampshire and consisting of James Archie, William H.E. Day, Wayne
Maddison, Christopher Meacham, F. James Rohlf, David Swofford, and myself.
When the programs run they ask you to choose the final plotting device and
to indicate whether there is a preview screen and if so what it is. The
choices for previewing are a subset of those available for plotting, and they
can be different (the most useful combination will be a previewing graphics
screen with a hard-copy plotter or printer).
Here are the choices, with some comments on each:
If your laser printer, supposedly Postcript-compatible, refuses to print
the plot file, you might consider whether the first line of the plot file,
which starts with "%!" needs to be altered somehow or eliminated. If your
Laserwriter is hooked to a Macintosh it will be necessary to persuade it to
print the plot file. The public-domain utility SendPS enables one to do that:
it is provided by us with the Macintosh executable version of PHYLIP. If you
are compiling your own Macintosh version you should try to get SendPS: it is
available in libraries of Macintosh public domain programs. I have heard that
it does not work with the new System 7 version of the Mac operating system, but
that there is on the Printers diskette of the System 7 distribution diskettes a
utility called Laserwriter Font Utility that can accomplish the same task.
A problem may arose in how to get the plot files to the plotting device or
printer. One has to copy them directly, but one should be careful to not let
your serial or parallel port strip off the high-order bits in the bytes if you
are using one of the options that generate nonprintable characters. This will
be true for most of the dot matrix printers and for bitmaps dumped to an HP
Laserjet. This can be a problem under Unix or PCDOS. If, for example, you
have a dot-matrix printer connected to a parallel port under PCDOS, to copy the
file PLOTFILE to the printer without losing the high-order bits, you must use
the /B switch on the COPY command:
A problem that may occur under some operating systems, particularly the
VMS operating system for DEC VAXes, is having a plot file with lines that
exceed some operating system limit such as 255 characters. This can happen if
you are using the Tektronix option. You should set your terminal type with
the command $ SET TERM/NOWRAP/ESCAPE which will allow Tektronix and DEC ReGIS
plots to successfully appear on your terminal. That way, if you have a
terminal capable of plotting one of these kinds of plots, the operating system
will not interfere with the process. It will not be possible to use files of
Tektronix commands as final plot files, however, as the TYPE command usually
used to get them to appear on the screen does not allow lines longer than 2048
bytes, and Tektronix plots are single lines longer than that.
Another problem is adding labels (such as vertical scales and branch
lengths) to the plots produced by this program. This may require you to use
the PCX, PICT, or Xfig file format and use a draw or paint program to add them.
I would like to add more fonts. The present fonts are recoded versions of
the Hershey fonts. They are legally publicly distributable. Most other font
families on the market are not public domain and I cannot afford to license
them for distribution. Some people have noticed that the Hershey fonts, which
are drawn by a series of straight lines, have noticeable angles in what are
supposed to be curves, when they are printed on modern laser printers and
looked at closely. This is less a problem than one might think since,
fortunately, when scientific journals print a tree it is usually shrunk so
small that these imperfections (and often the tree itself) are hard to see!
One more font that could be added from the Hershey font collection would
be a Greek font. If Greek users would find that useful I could add it, but my
impression is that they publish mostly in English anyway.
The C version of these programs consists of two C programs, "drawgram.c"
and "drawtree.c". Each of these has a common section of code called
"drawgrahics.c" and a common header file, "drawgraphics.h". IN addition the
Macintosh version requires two more files, "interface.c" and "interface.h".
All of the graphics commands that are common to both programs will be found in
"drawgraphics.c". The following instructions for writing your own code to
drive a different kind of printer, plotter, or graphics file format, require
you only to make changes in "drawgraphics.c". The two programs can then be
recompiled.
If you want to write code for other printers, plotters, or vector file
formats, this is not too hard. The plotter option "U" is provided as a place
for you to insert your own code. Chris Meacham's system was to draw
everything, including the characters in the names and all curves, by drawing a
series of straight lines. Thus you need only master your plotter's commands
for drawing straight lines. In procedure "plotrparms" you must set up the
values of variables "xunitspercm" and "yunitspercm", which are the number of
units in the x and y directions per centimeter, as well as variables "xsize"
and "ysize" which are the size of the plotting area in centimeters in the x
direction and the y direction. A variable "penchange" of a user-defined type
is set to "yes" or "no" depending on whether the commands to change the pen
must be issued when switching between plotting lines and drawing characters.
Even though dot-matrix printers do not have pens, penchange should be set to
"yes" for them. In PROCEDURE plot you must issue commands to draw a line from
the current position (which is at (xnow, ynow) in the plotter's units) to the
position (xabs, yabs), under the convention that the lower-left corner of the
plotting area is (0.0, 0.0). In procedures "initplotter" and "finishplotter"
you must issue commands to initialize the plotter and to finish plotting,
respectively. If the pen is to be changed an appropriate piece of code must be
inserted in procedure "penchange".
For dot matrix printers and raster graphics matters are a bit more
complex. The procedures "plotrparms", "initplotter", "finishplotter" and "plot"
still respectively set up the parameters for the plotter, initialize it, finish
a plot, and plot one line. But now the plotting consists of drawing dots into
a two-dimensional array called "stripe". Once the plot is finished this array
is printed out. In most cases the array is not as tall as a full plot: instead
it is a rectangular strip across it. When the program has finished drawing in
ther strip, it prints it out and then moves down the plot to the next strip.
For example, for Hewlett-Packard Laserjets we have defined the strip as 2550
dots wide and 20 dots deep. When the program goes to draw a line, it draws it
into the strip and ignores any part of it that falls outside the strip. Thus
the program does a complete plotting into the strip, then prints it, then moves
down the diagram by (in this case) 20 dots, then does a complete plot into that
strip, and so on.
To work with a new raster or dot matrix format, you will have to define
the desired width of a strip ("strpwide"), the desired depth ("strpdeep"), and
how many lines of bytes must be printed out to print a strip. For example
Toshiba P351 printers in graphics mode print strips of dots 1350 bits wide by
24 bits deep, each column of 24 bits printing out as consecutive four bytes
with 6 bits each. In that case, one prints out a strip by printing up to 1350
groups of 4 bytes. "strpdiv" is 4, and "strpwide" is 1350, and "strpdeep" is
24. procedure "striprint" is the one that prints out a strip, and has
special-case code for the different printers and file formats. For file
formats, all of which print out a single row of dots at a time, the variable
"strpdiv" is not used. The variable "dotmatrix" is set to "true" or "false" in
procedure "plotrparms" according to whether or not "strpdiv" is to be used.
procedure "plotdot" sets a single dot in the array "strip" to 1 at position
(xabs, yabs). The coordinates run from 1 at the top of the plot to larger
numbers as we proceed down the page. Again, there is special-case code for
different printers and file formats in that procedure. You will probably want
to read the code for some of the dot matrix or file format options if you want
to write code for one of them. Many of them have provision for printing only
part of a line, ignoring parts of it that have no dots to print.
I would be happy to obtain the resulting code from you to consider adding
it to this listing so we can cover more kinds of plotters, printers, and file
formats.
Trees
A D
\ E /
\ C / /
\ ! / /
\ ! / /
B \!/ /
\ o /
\ ! /
\ ! /
\ ! /
\ ! /
\!/
o
!
!
then in the tree file it is represented by the following sequence of printable
characters, starting at the beginning of the file:
(B,(A,C,E),D);
The tree ends with a semicolon. Everything after the semicolon in the input
file is ignored, including any other trees. The bottommost node in the tree is
an interior node, not a tip. Interior nodes are represented by a pair of
matched parentheses. Between them are representations of the nodes that are
immediately descended from that node, separated by commas. In the above tree,
the immediate descendants are B, another interior node, and D. The other
interior node is represented by a pair of parentheses, enclosing
representations of its immediate descendants, A, C, and E.
(,(,,),);
is allowed. Trees can be multifurcating at any level (while in many of the
programs multifurcations of user-defined trees are not allowed or restricted to
a trifurcation at the bottommost level, these programs do make any such
restriction).
(B:6.0,(A:5.0,C:3.0,E:4.0):5.0,D:11.0);
These programs will be able to make use of this information only if lengths
exist for every branch, except the one at the bottom of the tree.
((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700,
seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201,
weasel:18.87953):2.09460):3.87382,dog:25.46154);
(Bovine:0.69395,(Gibbon:0.36079,(Orang:0.33636,(Gorilla:0.17147,(Chimp:0.19268,
Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460);
(Bovine:0.69395,(Hylobates:0.36079,(Pongo:0.33636,(G._Gorilla:0.17147,
(P._paniscus:0.19268,H._sapiens:0.11927):0.08386):0.06124):0.15057):0.54939,
Rodent:1.21460);
();
((A,B),(C,D));
(Alpha,Beta,Gamma,Delta,,Epsilon,,,);
Plotters
Conversion from these formats to others is also possible. The graphics
conversion utility HiJaak, from Inset Systems (71 Commerce Drive, Brookfield,
Connecticut 06804, (203) 775-5866) is a PCDOS program that converts numerous
graphic file formats on input and output. It can read many formats, including
the HPGL format and write many formats. It is available from many software
discount houses. There is also a public-domain program by Jef Poskanzer called
"PBMPLUS" that interconverts many bitmap formats.
Problems Copying Files to Printers
COPY/B PLOTFILE PRN:
The VAX VMS Line Length Problem
Other problems and opportunities
Writing Code for a new Plotter, Printer or File Format
Maintained 15 Jul 1996 -- by Martin Hilbers(e-mail:M.P.Hilbers@dl.ac.uk)
