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 ( | + | '''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. |
− | 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 | + | 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 == | + | ==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 == | + | ==Online help== |
''note: taken from the <tt>njplot.help</tt> file.'' | ''note: taken from the <tt>njplot.help</tt> file.'' | ||
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=== Subtree up === | === Subtree up === | ||
− | When a | + | 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)== |
− | + | <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/> | |
− | [[Category: | + | ==See also== |
+ | *[http://genome.cse.ucsc.edu/cgi-bin/phyloGif phyloGif Interactive Phylogenetic Tree Gif Maker] | ||
+ | |||
+ | ==External links== | ||
+ | *[http://pbil.univ-lyon1.fr/software/njplot.html Official '''NJplot''' site] | ||
+ | *[ftp://ftp.ebi.ac.uk/pub/software/njplot/ mirror on EBI] | ||
+ | |||
+ | [[Category:Graphics software]] | ||
[[Category:Phylogenetics]] | [[Category:Phylogenetics]] | ||
+ | [[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.
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