J. Biomedical Science and Engineering, 2011, 4, 90-93 JBiSE
doi:0.4236/jbise.2011.42012 Published Online February 2011 (http://www.SciRP.org/journal/jbise/).
Published Online February 2011 in SciRes. http://www.scirp.org/journal/JBiSE
PHYLIP-GUI-Tool (PHYGUI): adapting the functions of the
graphical user interface for the PHYLIP package
Yukinori Eguchi
Research Laboratory Center, F aculty of Medicine, University of the Ryukyus, Okinawa, Japan.
Received 3 December 2010; revised 27 December 2010; accepted 4 January 2011.
ABSTRACT
The PHYGUI for the PHYLIP package is a simple
and user-friendly piece of software that acts such as a
Windows based graphical-user-interface for the PHY-
LIP phylogenetic data analysis package. PHYLIP is a
useful and powerful tool for phylogenetic research
that is regretfully operated using a character-user-
interface. Therefore, PHYLIP is difficult for beginner
level users. The PHYGUI for PHYLIP adds a GUI
function, which makes it a more user-friendly and
powerful tool. PHYGUI runs on multiple platforms
such as MS-Windows and X windows on Mac OS-X
and Linux systems and is mainly operated using a
mouse. The input data file and the output result data
files can be viewed and edited using internal or ex-
ternal text editors, which c an be accessed via a button
on the PHY GUI for PHYLIP.
Keywords: PHYLIP; Phylogeny; GUI; Software
1. INTRODUCTION
The PHYLIP software package [1] is a useful and pow-
erful tool for phylogenetic analysis and is probably the
most widely distributed phylogeny package. The PHY-
LIP package contains several programs for inferring
phylogenies developed by Joe Felsenstein. These pro-
grams are controlled through a menu using a character
based user interface. The menu contains options that are
set by the user and also allows them to start phylogeny
computations. The programs read data from a text file,
which the user is able to prepare using any text editor.
The majority of the programs look for data in a text file
called “infile”. Also, the PHYLIP programs are able to
run in the background, take their input data from a se-
quence data file, put their output into a text file called
“screenout”, and use a text file called “input” to store
user input. Regretfully, the PHYLIP package uses a
character-based user-interface. If the PHYLIP package
had a graphical-user-interface, it would be more user-
friendly, especially for beginners. The PHYGUI for PHY-
LIP is a graphical-user-interface (GUI) for the PHYLIP
package. The PHYGUI for PHYLIP is helpful for be-
ginners as it makes PHYLIP more user-friendly. In addi-
tion, the PHYGUI for PHYLIP improves the “input-file”
used for batch-background processing by the PHYLIP
programs as it generates an “input-file” that contains the
input data file name, some option commands, and the
corresponding par ameter values.
2. METHODS
2.1. Platform Requirements
PHYGUI was developed using a GUI application in Java
1.6 and therefore runs on Java VM 1.6. The PHYGUI is
executable on some versions of MS-Windows (XP, Vista,
7) and X windows on Mac OS-X 10.6, and Linux (Ub-
untu 9.10) systems.
2.2. Installation of the PHYGUI Program
The installation of the PHYGUI program involves two
steps. The PHYGUI requires the PHYLIP package to be
installed; therefore, the first step is to install the PHYLIP
package. The default directory for installation is “c:/
phtlip3.5” on Windows systems and “/phylip3.5” on
Mac OS-X and Linux systems. The PHYGUI program
also requires a phygui.int file to run on all systems, an
exephy.bat file to run on MS Windows systems, and an
exephy.sh file to run on Mac OSX and Ubuntu systems.
In the second step, the PHYGUI program, “phygui.jar”,
is copied to an arbitrary directory. These necessary files
can be downloaded from the PHYGUI directory as de-
scribed be l ow.
2.3. Running the PHYGUI Program
The PHYGUI program is started on MS-Windows sys-
tems by “double clicking” its icon. It is useful to p lace a
shortcut icon linked to the PHYGUI program on the
desktop or in a convenient directory. On Mac OS-X or

Y. Eguchi / J. Biomedical Science and Engineering 4 (2011) 90-93 91
Linux systems, the PHYGUI prog ram is run through the
X-windows application. To run the program, enter “java
–jar phygui.jar” into the command line of the terminal
window in X-windows. The PHYGUI program then
launches the main menu window in X-system.
3. RESULTS AND DISCUSSION
The PHYGUI consists of a setup menu, a main menu
window, and several analysis windows and has the fol-
lowing features and functions:
3.1. Setup Menu
The setup menu window can be launched by selecting it
from the pull-down menu in the main menu window. The
setup menu window allows the user to specify the direc-
tories where the executable files for the PHYLIP package
and the analysis data files are stored and to switch be-
tween the internal viewer and editing tool or an external
editor. The internal editor allows the user to view, edit,
rename, save, and pri ntout results or input data.
3.2. Main Menu Window
The main menu window is the top window in PHYGUI
and is used to select a program from the PHYLIP pack-
age (Figure 1A). It is possible to select “setup”, “about”,
or “exit” from the main menu window. The “setup”
menu allows the user to change some parameters such as
the directories where executable PHYLIP software files,
input files, and output files are stored. The phylogeny
program in the PHYLIP package is selected by clicking
on a radio button in the main menu window. The analy-
sis window, which is used to set optional parameters, is
automatically launched after a phylogeny program has
been selected from the PHYLIP package.
3.3. Analysis Windows
The selectable options for the PHYLIP package are
complicated, and so it is difficult to show all of the op-
tions for the PHYLIP package in one analysis window.
Therefore, the PHYGUI program has several analysis
panels (Figure 1(b)), the panel for “molecular sequence
methods” for DNApars, ProtPars, and 13 other programs;
the panel f or “distance matrix methods” for Fitch, Kitsch,
and Neighbor; the panel for “distance characters meth-
ods” for Pars, Dollp, and 6 other programs; the panel for
“gene frequencies and continuous characters” for Contml,
Contdist, and Gendist; the panel for “consensus, tree
editing, and tree distances” for Consense, Treedist, and
Move; and the panel for “Interactive methods” for
DNAmove, Dolmove, and Move. Each analysis window
contains all the optional parameters for the PHYLIP
package, and the necessary options for individual phy-
logeny programs are automatically selected. The input
data file can be selected in a directory/file view window
using a mouse, and the various optional parameters are
selected via radio buttons using a mouse. However,
some opt i ons require numer i c al values to be en t ered.
3.4. Input File and Output File
The input file is stored in PHYLIP format, which is a
type of text file. These text files can be viewed or edited
using the internal editing tool or an external text editor,
and a compatible text editor can be chosen via the
menu-setup procedure. The output files produced by the
programs can also be viewed using the internal editing
tool or an extern al text editor and show the resu lts of the
phylogeny analyses (Figure 1(c)). The “outfile” f ile co n-
tains the results of the calculations performed by a
PHYLIP program and can be viewed in the chosen
manner by clicking on the “outfile” button in the analy-
sis window. The “outtree” file is the tree produced by a
PHYLIP program and can be viewed with a text editor
by clicking on the “outtree” button in the analysis win-
dow. These outfile and outtree files can be renamed or
printed in the internal text viewer using the “save as…”
and “print” options, respectively.
The available software packages for phylogenetic
analysis include PHYLIP, PAUP*[2], and MEGA [3,4].
PAUP* and MEGA have graphical user interfaces that
can be operated using a mouse. However, PHYLIP has a
character-based user interface that is operated using a
keyboard. Therefore, the PHYLIP package is more dif-
ficult to use than PAUP* or MEGA for beginner level
users. The PHYGUI provides a graphical user interface
for the PHYLIP package that is operated using a mouse
and runs on Windows, Mac, and Linux systems. The
combination of the PHYLIP package and PHYGUI al-
lows the phylogen y software to be operated easily, which
(a)
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opyright © 2011 SciRes. JBISE

Y. Eguchi / J. Biomedical Science and Engineering 4 (2011) 90-93 92
(b)
(c)
Figure 1. The main menu and analysis windows of the PHYGUI program. Panel (a) shows the main PHYGUI window in Windows 7
with the “dnapars” program selected. The windows below show the options for the selected program. Panel (b) shows the analysis
window for the “dnapars” program running on Mac OSX. The initial conditions of the analysis window, showing the “Infile select”
box and “Select” button. When a data file is selected, the possible options become highlighted. These options automatically change
for each program. Panel (c) shows the viewer window for the “dnapars” program running on Ubuntu.

Y. Eguchi / J. Biomedical Science and Engineering 4 (2011) 90-93 93
is very useful for begi n ner s.
In this paper, we used PHYLIP package version 3.68,
which can be downloaded from the PHYLIP website
(http://evolution.gs.washington.edu/phylip.html). The PHY-
GUI interface is available by email on request from:
[e-mail] and can also be downloaded
from the following website:
http://wwwrlc.med.u-ryukyu.ac.jp/PHYGUI.
REFERENCES
[1] Felsenstein, J. (2005) PHYLIP (phylogeny inference
package) version 3.6. Distributed by Author. Department
of Genome Sciences, University of Washington, Seattle.
http://evolution.genetics.washington.edu/phylip.html
[2] Swofford, D.L. (2001) PAUP*: Phylogenetic analysis
using parsimony and other methods. Sinauer Associates,
Sunderland, MA. http://paup.csit.fsu.edu/
[3] Kumar, S., Dudley, J., Nei, M. and Tamura, K. (2008)
MEGA: A biologist-centric software for evolutionary
analysis of DNA and protein sequences. Briefings in
Bioinformatics, 9, 299-306. doi:10.1093/bib/bbn017
[4] Tamura, K., Dudley, J., Nei, M. and Kumar, S. (2007)
MEGA4: Molecular evolutionary genetics analysis
(MEGA) software version 4.0. Molecular Biology and
Evolution, 24, 1596-1599.
doi:10.1093/molbev/msm092
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opyright © 2011 SciRes. JBISE