Propositions concerning NH treefiles

higgins at ebi.ac.uk higgins at ebi.ac.uk
Mon Apr 29 05:23:54 EST 1996


In article <4lqp04$hi0 at babyblue.CS.YALE.EDU>, peter at carrot.mcb.uconn.edu (Peter) writes:
> In article <4lo1rb$bc8 at lyra.csx.cam.ac.uk>, 
> strimmer at zi.biologie.uni-muenchen.de says...
>>
>>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 boots
> 
> //stuff deleted
> 
> Korbinian, CLUSTALW and TREEVIEW both handle bootstrap values and branch 
> lengths simultaneously.  The branch lengths is given after a ":", the 
> bootstrap values are given as "internal labels" directly after the closing 
> parenthesis of the pertaining group.
> 		Peter
> 
> 
> 

With Clustal W we followed
the "extended" NH format used by TREETOOL to allow the
bootstrap values to be included in the files (as labels).  This format is also
used by NJplot by Manolo Gouy.   It is nice because it allows one
to print the bootstrap values in convenient places but is not
nice becase it is not a "standard" format.    The great thing
about using the NH format in the first place is that other packages
(especially PHYLIP) can share your trees.  This breaks down if people
start using different "flavours".  

Joe Felsenstein mentions in a different followup post that you could use
the proposed label format of NH to do this.  That would indeed keep
us all happy as long as everyone switched to it.  Go to it Joe :-).


Des Higgins


> ********************************************
>   J. Peter Gogarten
>   University of Connecticut
>   Dept. Molecular and Cell Biology
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