Difference between revisions of "NJplot"

Revision as of 07:11, 20 April 2007

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.

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.

External links

• Official NJplot site