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>>>About njplot
Version: ??
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 PDF or PostScript files.
Input trees can be with/without branch lengths, with/without bootstrap
values, rooted or unrooted. Binary as well as multibranched trees are accepted.
njplot is available at
http://pbil.univ-lyon1.fr/software/njplot.html
for MAC, PC under MS-Windows and several unix platforms.
njplot uses the Vibrant library by J. Kans.
Some versions of njplot use the PDFLib Lite library (http://www.pdflib.com)
under the "Open Source Developer Exemption" of the PDFlib Lite License Agreement.
>>>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 as PDF/PostScript: To save the tree plot in PDF/PostScript format.
Save rooted/unrooted tree: To save the tree in a file with/without its current rooting.
Print: [Mac & Windows ONLY] it does print your tree.
>>>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 as PDF" item of menu "File".
Pagecount (x): sets the number of pages used by "Save as PDF".
>>>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 "Full 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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