Propositions concerning NH treefiles

higgins at ebi.ac.uk higgins at ebi.ac.uk
Mon Apr 29 06:11:28 EST 1996


In article <1996Apr29.102354 at ebi.ac.uk>, higgins at ebi.ac.uk writes:
> 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 :-).
> 

Sorry, me again (now I am talking to myself).  I read what Joe said again
and it looks like those labels were always in the NH format.  The problem
is finding the format definition.  

Des


> 
> Des Higgins
> 
> 
>> ********************************************
>>   J. Peter Gogarten
>>   University of Connecticut
>>   Dept. Molecular and Cell Biology
>>   75 North Eagleville Rd.
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>>   E-Mail: gogarten at uconnvm.uconn.edu
>>           or peter at carrot.mcb.uconn.edu 
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>> 



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