File: njplot.help

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njplot 2.4-1
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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.