File: njplot.html

package info (click to toggle)
njplot 2.4-7
  • links: PTS, VCS
  • area: main
  • in suites: stretch
  • size: 404 kB
  • ctags: 659
  • sloc: ansic: 6,164; makefile: 75; sh: 19
file content (125 lines) | stat: -rw-r--r-- 4,787 bytes parent folder | download | duplicates (5)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
<HEAD>
<TITLE>NJplot</TITLE>
</HEAD>
<BODY BGCOLOR="#F0F0F0">
<CENTER>
<H1>NJplot</H1>
NEW: NJplot plots trees in PDF and PostScript formats (not for MacOS).
<br>NEW: NJplot allows to open several tree windows.
<br>NEW: NJplot can draw multibranched trees with or without branch lengths.
</CENTER>
<HR>
<P>
NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the
<a href=http://evolution.genetics.washington.edu/phylip/newicktree.html>Newick</a> phylogenetic tree format (<I>e.g.</I>, the format used by the
PHYLIP package). NJplot is especially convenient for rooting the unrooted trees
obtained from parsimony, distance or maximum likelihood tree-building methods.</p>
<P>
A screen shot of the main window of njplot is available 
<A HREF="/binaries/njplot.gif">here</A>.
<H3>Use of NJPlot</H3>
Any rooting of the unrooted tree can be interactively specified using the mouse.
NJplot also allows zooming, branch swapping, display of bootstrap scores and
printing in the PDF format. NJplot can therefore be used as a graphical
extension of any package of phylogenetic programs which employs the standard
tree format for storing trees (<I>i.e.</I>, with most such packages). 
<H3>Download NJplot</H3>
Executables and full <A HREF="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/njplot.tar.gz">source code</a>
can be downloaded through our
<A HREF="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot">FTP server</A>.
You may also use the following table to directly access the version
corresponding to your computer:
<P></p>
<center>
<TABLE BORDER=4 CELLPADDING=8>

<TR ALIGN=LEFT>
<TD>
<H3>
<IMG ALIGN=BOTTOM SRC="/binaries/MacOSX_Universal_40px.gif">
<A HREF="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/njplot.zip">MacOS X</A>
<br>
<IMG ALIGN=BOTTOM SRC="/binaries/apple_logo.png">
<A HREF="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/njplotMAC.hqx">MacOS (8,9)</A>
</H3>
</TD>

<TD>
<H3>
<IMG ALIGN=BOTTOM SRC="/binaries/linux.gif">
<A HREF="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/njplot.linux">Linux on PC</A>
<br><font size=2>in case of <A HREF=#FONTPROBLEM>font problem</A></font>
<br><font size=2>Use without X11 display: <A HREF=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/newicktopdf>newicktopdf</A></font>
</H3>
</TD>

<TD>
<H3>
<IMG ALIGN=BOTTOM SRC="/binaries/win_logo.png">
<A HREF="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/njplotWin95.exe">MS Windows</A>
</H3>
</TD>

<TD>
<H2>
<IMG ALIGN=BOTTOM SRC="/binaries/sun.gif">
<A HREF="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/njplot.solaris">Sun-Solaris</A>
</H3>
</TD>

<TD>
<H3>
<IMG ALIGN=BOTTOM SRC="/binaries/hp.gif">
<A HREF="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/njplot.alpha">HP Alpha</A>
</H3>
</TD>

</TR>

</TABLE>

</CENTER>
<P>The Mac and Windows versions are self-extracting archives which include
an example file, help information, and the unrooted program that draws
unrooted trees. The Windows version is for any MS Windows version except 3.*.</P>
<P>
For unix versions, get also an 
<A HREF="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/test.ph">example tree file</A> and the 
<A HREF="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/njplot.help">on-line help file</A>.


<p><a name=FONTPROBLEM></a></P>
<b>Note for unix/linux users</b>: In case of problem with default fonts, the font used by menus
and buttons can be changed through the resource mechanism:
<br>- add to your $HOME/.Xdefaults file the single line
<br><tt>Vibrant.systemfont : Helvetica,14,b</tt>
<br>and activate the change by running command <tt>xrdb -merge $HOME/.Xdefaults</tt>
<br>- you may change the font name (times, courier, fixed) and size.
<br>- For that change to apply systemwide, create a file named Vibrant and containing the above line
in directory /usr/X11R6/lib/X11/app-defaults or in a directory pointed to by environment variable 
XAPPLRESDIR.


<H3>Use as a helper application</H3>
NJplot can be used as a standalone application or as a helper
application when using the World Wide Web. In this case, prospective
users must <A HREF="/help/helpers.html">configure</A> their WWW browser
in a way to make it able to recognize the MIME-type associated to the data
read by NJplot: <B><I>chemical/njplot</I></B>. 
<H3>Reference</H3>
If you use NJplot in a published work, please cite the following
<A HREF="http://dx.doi.org/10.1016/0300-9084(96)84768-7">reference</A>:
<DL>
<DD>
Perri&egrave;re, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system
for biological sequence banks. <I>Biochimie</I>, <B>78</B>, 364-369.
</DD>
</DL>
<HR>
<ADDRESS>
<A HREF="/comments.html">If you have problems or comments...</A>
<P></P>
<A HREF="/pbil.html"><IMG SRC="/binaries/home.gif"></A>
<I>Back to PBIL home page</I>
</ADDRESS>
</BODY>