njplot.help

是有关基因比对的经典算法的实现。这对于初学计算生物学的人是非常重要的算法。

>>>About njplot
Written by M. Gouy ([e-mail]).

Phylogenetic trees read from Newick formatted files can be displayed,
re-rooted, saved, printed and plotted to PostScript files.
Input trees can be with/without branch lengths, with/without bootstrap
values, rooted or unrooted. Only binary trees are accepted.

njplot is available at ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot 
for MAC, Windows95 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.

Save tree:  To save the tree in a file with its current rooting.

Print:  use Paper:Page count to set the number of pages for printout.
>>>Menu Edit
Copy:     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 "Print" and "Save plot" of menu "File".

Pagecount (x): sets the number of pages used by "Print" and "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.