Thanks to all who responded to my question. I never recommend Pileup's
dendrogram for evolutionary relationship but in this particular case, it's
what the user wanted and the length of the branches (perhaps coincidentally)
seem to correspond to the respective percent identity.
I'm very grateful to you for taking the time to answer and also to Eric Cabot
at GCG who clarified what the problem was (ie. scoring matrices).
If there's interest, I'll post his reply here.
In article <E0yH3Rb-0003UD-00 at mail1.uct.ac.za>, ed at MOLBIOL.UCT.AC.ZA ("Ed Rybicki") writes:
>>> Anyway, this tree can not be used as a phylogenetic tree,
>> I can't recommand using this tree for something else than
>> checking PileUp alignment order. Just have a look at PAUP
>> Have to agree: the "tree" you get out of PileUp - however pretty - is
> only as much of a tree as the dendrogram Clustal uses to guide its
> subsequent alignment; in other words, it is a preliminary dendrogram,
> based on pairwise sequence alignements prior to the generation of the
> aligned matrix of sequences. Which we throw away...!
>> Although I would not look at PAUP, given that we have ClustalW and
>> Ed Rybicki, PhD
> Dept Microbiology | ed at molbiol.uct.ac.za> University of Cape Town | rybicki at uctvms.uct.ac.za> Private Bag, Rondebosch | phone: x27-21-650-3265
> 7700, South Africa | fax: x27-21-689 7573
> WWW URL: http://www.uct.ac.za/microbiology/ed.html>> "Every year is getting shorter, never seem to find the time..."