Hi Giacomo and others,
I have run the network in Arlequin as well but that is a minimum
spanning method not statistical parsimony, correct? I am unfamiliar
with Hapstar. I think that the reason the haploNet command doesn't
produce loops may have something to do with the order of sequences in
the alignment file. I am working on rebuilding the network with the
sequences in a different order to see if the same topology is recovered.
Patrick
On Mar 29, 2011, at 10:28 AM, Patrick Flight wrote:
Hello r-sig-phylo,
I am using the haploNet command of the excellent pegas package to
construct an mtDNA haplotype network with 79 nodes. When I generate
the network I am able to identify the limits of parsimony from the
accompanying table. However, I don't quite understand why this
network contains no loops (79 nodes 78 edges). When I make the
network in TCS the parsimony limits are the same (7 steps), but
there are many loops in the network. The documentation refers to the
Templeton et al. 1992 paper and, short of identifying recombination
to break loops, I couldn't find hard and fast rules for breaking
loops (I may have missed them). I know that some post hoc rule
exist, such as favoring links to high frequency and geographically
close haplotypes, but I was wondering how haploNet deals with these
loops. Does it present 1 of the maximum parsimony trees?
Thanks in advance,
Patrick
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