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>>>About njplot
Written by M. Gouy (mgouy@biomserv.univ-lyon1.fr).
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. Only binary trees are accepted.
njplot is available by anonymous FTP at pbil.univ-lyon1.fr in directory
/pub/mol_phylogeny/njplot/ for MAC, PC under Windows95/NT and several unix
platforms.
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 & 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 subtree is being displayed, allows to add one more node towards the
root in the displayed tree part.
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