NJplot
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.
Contents
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
- ↑ 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
