Propositions concerning NH treefiles

John Hunt jahunt at hawaii.edu
Fri Apr 26 22:01:27 EST 1996


The suggestions that you make seem to have been implimented by Des 
Higgins in Clustal, and the Macintosh based TreeView by Rod Page will 
view the NH files with both distances and bootstrap 
values.(http://taxonomy.zoology.gla.ac.uk/rod/treeview.html) in addition 
Andrey Zharkikh has modofied the output of his bootstrap programs so that 
they conform to Des Higgins standard. These are available by ftp at 
hgc6.sph.uth.tmc.edu/pub/zharkikh/bootstrap.
I have successfully compiled the latter programs for the Mac.

John Hunt

On Thu, 25 Apr 1996, Korbinian Strimmer wrote:

> I'd like to put the following two propositions concerning NH treefiles
> to the public for discussion:
> 
> a) Sometimes you need to draw a tree with edge lengths *and* corresponding bootstrap
>    values for each internal branch. For example, consider this tree with edge lengths:
> 
>    (LungfishAu:0.1246,(LungfishSA:0.1338,LungfishAf:0.1324):0.0769,(
>    (((Platypus:0.1441,Opossum:0.1302):0.0380,((Mouse:0.0566,Rat:0.0717)
>    :0.1017,(((Cow:0.0803,Whale:0.0935):0.0334,Seal:0.0848):0.0267,Human:0.1514)
>    :0.0355):0.0495):0.0865,((((Crocodile:0.1948,Bird:0.1546):0.0560,Sphenodon:0.2029)
>    :0.0239,Lizard:0.2302):0.0362,Turtle:0.1508):0.0581):0.0842,Frog:0.1664)
>    :0.0619);
> 
>    and the same tree with bootstraps for it internal branches:
> 
>    (LungfishAu,(LungfishSA,LungfishAf):100,((((Platypus,Opossum):100,
>    ((Mouse,Rat):100,(((Cow,Whale):100,Seal):100,Human):98):99):100,
>    ((((Crocodile,Bird):100,Sphenodon):92,Lizard):72,Turtle):100):100,
>    Frog):99);
> 
>    At the moment, it is not possible to have *both* information in one treefile, and it is
>    not possible to print let's say a phenogram with bootstraps.
> 
>    I therefore would like to propose that the current NH convention should be extended
>    to allow for more than one : extension. The tree drawing programs (DRAWTREE, DRAWGRAM,
>    TreeView) could then allow the user to specify the task of each entry, say the first
>    is the edge length, the second entry is the bootstrap value for each (internal) branch.
> 
>    Another possibility would be that the tree drawing programs allow for the input of 2 treefiles
>    at the same time to generate 1 picture of a tree. ( Probably this is even a better solution
>    than allowing for more than one : extension)
> 
> 
> b) As another extension of the NH scheme I'd like to propose that treefiles should *always*
>    look like this:
> 
>      1
>    (LungfishAu:0.1246,(LungfishSA:0.1338,LungfishAf:0.1324):0.0769,(
>    (((Platypus:0.1441,Opossum:0.1302):0.0380,((Mouse:0.0566,Rat:0.0717)
>    :0.1017,(((Cow:0.0803,Whale:0.0935):0.0334,Seal:0.0848):0.0267,Human:0.1514)
>    :0.0355):0.0495):0.0865,((((Crocodile:0.1948,Bird:0.1546):0.0560,Sphenodon:0.2029)
>    :0.0239,Lizard:0.2302):0.0362,Turtle:0.1508):0.0581):0.0842,Frog:0.1664)
>    :0.0619);
> 
>    This means that in the first line there should always be a number indicating the number
>    of trees following. This would have the advantage that input trees and output trees have
>    the same format (DNAML 4.0!)  und you could just rename the corresponding files. It would
>    also create a compatibility between PHYLIP tree files and MOLPHY topology files.
> 
> 
> What do you think about these two propositions? 
> 
> 
> Korbinian Strimmer
> 
> 



More information about the Mol-evol mailing list