Difference between revisions of "NJplot"

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'''NJplot''' is a tree drawing program able to draw any phylogenetic tree expressed in the [[Newick phylogenetic tree format]] (e.g., the format used by the [[PHYLIP]] package). It was written by M. Gouy (see reference below). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
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'''NJplot''' is a tree drawing program able to draw any phylogenetic tree expressed in the [[Newick phylogenetic tree format]] (e.g., the format used by the [[PHYLIP]] package). It was written by M. Gouy.<ref name="Perriere1996">Perrière G, Gouy M (1996). "WWW-Query: An on-line retrieval system for biological sequence banks". ''Biochimie'' '''78''':364-369. {{doi|10.1016/0300-9084(96)84768-7}}</ref> NJplot is especially convenient for rooting the un-rooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
  
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Phylogenetic trees read from Newick formatted files can be displayed, re-rooted, saved, and plotted to PostScript (or PICT for the Macintosh) files. Input trees can be with/without branch lengths, with/without bootstrap values, rooted or unrooted. Binary as well as multibranched trees are accepted.
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Phylogenetic trees read from Newick formatted files can be displayed, re-rooted, saved, and plotted to [[PostScript]] (or PICT for the Macintosh) files. Input trees can be with/without branch lengths, with/without bootstrap values, rooted or un-rooted. Binary as well as multi-branched trees are accepted.
  
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== Availability ==
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==Availability==
 +
NJplot is available at http://pbil.univ-lyon1.fr/software/njplot.html for MAC, PC (under Windows95/NT/XP), and several Unix/[[Linux]] platforms.
  
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NJplot is available at http://pbil.univ-lyon1.fr/software/njplot.html for MAC, PC (under Windows95/NT/XP), and several Unix/Linux platforms.
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Latest version: 2.4 (2012-01-04)
  
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== Online help ==
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==Online help==
 
''note: taken from the <tt>njplot.help</tt> file.''
 
''note: taken from the <tt>njplot.help</tt> file.''
  
 
NJplot uses the Vibrant library by J. Kans.
 
NJplot uses the Vibrant library by J. Kans.
  
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=== Menu File ===
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=== >Menu: File ===
 
; Open : To read a tree file in the Newick format (i.e., the file format used for trees by Clustal, PHYLIP, and other programs).
 
; Open : To read a tree file in the Newick format (i.e., the file format used for trees by Clustal, PHYLIP, and other programs).
 
; Save plot : To save the tree plot in PostScript format, or in the PICT format for the Macintosh.
 
; Save plot : To save the tree plot in PostScript format, or in the PICT format for the Macintosh.
 
; Save tree : To save the tree in a file with its current rooting.
 
; Save tree : To save the tree in a file with its current rooting.
  
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=== Menu Edit ===
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=== >Menu: Edit ===
 
; Copy : [Mac and Windows ONLY!] Copies the current tree plot to the Clipboard so that the plot can be pasted to another application.
 
; Copy : [Mac and Windows ONLY!] Copies the current tree plot to the Clipboard so that the plot can be pasted to another application.
 
; Paste : If the clipboard contains a parenthesized tree, this tree will be plotted.
 
; Paste : If the clipboard contains a parenthesized tree, this tree will be plotted.
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; Again : Redisplay in red names matching the string entered in a previous Find operation.
 
; Again : Redisplay in red names matching the string entered in a previous Find operation.
  
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=== Menu Font ===
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=== >Menu: Font ===
 
Allows to change the font face and size used to display tree labels.
 
Allows to change the font face and size used to display tree labels.
  
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=== Menu Paper ===
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=== >Menu: Paper ===
 
Allows to set the paper size used by the "Save plot" item of menu "File".
 
Allows to set the paper size used by the "Save plot" item of menu "File".
  
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=== Subtree up ===
 
=== Subtree up ===
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When a subtree is being displayed, allows to add one more node towards the root in the displayed tree part.
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When a sub-tree is being displayed, allows to add one more node towards the root in the displayed tree part.
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 +
==Example tree file (input)==
 +
<pre>
 +
(
 +
(
 +
(
 +
(
 +
GlnRS[Ec]:0.22184,
 +
GlnRS[Sc]:0.22033)
 +
40:0.17723,
 +
(
 +
(
 +
(
 +
TrpRS[Ec]:0.16684,
 +
(
 +
TrpRS[Bst]:0.10637,
 +
TrpRS[Bsu]:0.10451)
 +
970:0.05425)
 +
10:0.10491,
 +
TrpRS[Scm]:0.25223)
 +
20:0.14764,
 +
(
 +
(
 +
(
 +
TyrRS[Bst]:0.14456,
 +
TyrRS[Ec]:0.14116)
 +
30:0.15731,
 +
TyrRS[Ncm]:0.29167)
 +
991:0.06216,
 +
TyrRS[Bsu]:0.35621)
 +
992:0.05942)
 +
999:0.07979)
 +
1000:0.09412,
 +
GluRS[Ec]:0.25282)
 +
610:0.02439,
 +
GluRS[Rm]:0.24251,
 +
(
 +
GluRS[Bst]:0.13448,
 +
GluRS[Bsu]:0.11723)
 +
99:0.07382);
 +
</pre>
  
 
==References==
 
==References==
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* Perrière G. and Gouy M (1996). WWW-Query: An on-line retrieval system for biological sequence banks. ''Biochimie'' '''78''':364-369.
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<references/>
 +
 
 +
==See also==
 +
*[http://genome.cse.ucsc.edu/cgi-bin/phyloGif phyloGif Interactive Phylogenetic Tree Gif Maker]
  
 
==External links==
 
==External links==
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* [http://pbil.univ-lyon1.fr/software/njplot.html Official ''NJplot'' site]
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*[http://pbil.univ-lyon1.fr/software/njplot.html Official '''NJplot''' site]
 +
*[ftp://ftp.ebi.ac.uk/pub/software/njplot/ mirror on EBI]
  
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[[Category:Academic Research]]
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[[Category:Graphics software]]
 +
[[Category:Phylogenetics]]
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[[Category:Bioinformatics]]

Latest revision as of 02:42, 13 July 2012

NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). It was written by M. Gouy.[1] NJplot is especially convenient for rooting the un-rooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.

Phylogenetic trees read from Newick formatted files can be displayed, re-rooted, saved, and plotted to PostScript (or PICT for the Macintosh) files. Input trees can be with/without branch lengths, with/without bootstrap values, rooted or un-rooted. Binary as well as multi-branched trees are accepted.

Availability

NJplot is available at http://pbil.univ-lyon1.fr/software/njplot.html for MAC, PC (under Windows95/NT/XP), and several Unix/Linux platforms.

Latest version: 2.4 (2012-01-04)

Online help

note: taken from the njplot.help file.

NJplot uses the Vibrant library by J. Kans.

>Menu: File

Open 
To read a tree file in the Newick format (i.e., the file format used for trees by Clustal, PHYLIP, and other programs).
Save plot 
To save the tree plot in PostScript format, or in the PICT format for the Macintosh.
Save tree 
To save the tree in a file with its current rooting.

>Menu: Edit

Copy 
[Mac and Windows ONLY!] Copies the current tree plot to the Clipboard so that the plot can be pasted to another application.
Paste 
If the clipboard contains a parenthesized tree, this tree will be plotted.
Clear 
Clears the current plot so that new tree data can be pasted.
Find 
To search for a taxon in tree and display it in red. Enter a (partial) name, case is not significant.
Again 
Redisplay in red names matching the string entered in a previous Find operation.

>Menu: Font

Allows to change the font face and size used to display tree labels.

>Menu: Paper

Allows to set the paper size used by the "Save plot" item of menu "File".

Pagecount (x) 
sets the number of pages used by "Save plot".

Operations

Full tree 
Normal tree display of entire tree
New outgroup 
Allows to re-root the tree. The tree becomes displayed with added # signs. Clicking on any # will set descending taxa as an outgroup to remaining taxa.
Swap nodes 
Allows to change the display order of taxa. The tree becomes displayed with added # signs. Clicking on any # will swap corresponding taxa.
Subtree 
Allows to zoom on part of the tree. The tree becomes displayed with added # signs. Clicking on any # will limit display to descending taxa. Select "Show tree" to go back to full tree display.

Display

Branch lengths 
If the tree contains branch lengths, they will be displayed. For readability, very short lengths are not displayed.
Bootstrap values 
If the tree contains bootstrap values, they will be displayed.

Subtree up

When a sub-tree is being displayed, allows to add one more node towards the root in the displayed tree part.

Example tree file (input)

(
(
(
(
GlnRS[Ec]:0.22184,
GlnRS[Sc]:0.22033)
40:0.17723,
(
(
(
TrpRS[Ec]:0.16684,
(
TrpRS[Bst]:0.10637,
TrpRS[Bsu]:0.10451)
970:0.05425)
10:0.10491,
TrpRS[Scm]:0.25223)
20:0.14764,
(
(
(
TyrRS[Bst]:0.14456,
TyrRS[Ec]:0.14116)
30:0.15731,
TyrRS[Ncm]:0.29167)
991:0.06216,
TyrRS[Bsu]:0.35621)
992:0.05942)
999:0.07979)
1000:0.09412,
GluRS[Ec]:0.25282)
610:0.02439,
GluRS[Rm]:0.24251,
(
GluRS[Bst]:0.13448,
GluRS[Bsu]:0.11723)
99:0.07382);

References

  1. ↑ Perrière G, Gouy M (1996). "WWW-Query: An on-line retrieval system for biological sequence banks". Biochimie 78:364-369. DOI:10.1016/0300-9084(96)84768-7

See also

External links

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