Patrick, I am working on these kinds of issues as well. If you use Arlequin, or Hapstar to make networks, you will not get loops either, at least when you use the primary haplotype. TCS does keep loops, and separates networks without connections.
Giacomo On Mar 29, 2011, at 7:28 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 > > _______________________________________________ > R-sig-phylo mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Giacomo Bernardi Professor, Department of Ecology and Evolutionary Biology University of California Center for Ocean Health, Long Marine Lab 100 Shaffer Road Santa Cruz, CA 95060, USA Tel: office 831 459 5124 Tel: lab 831 459 1282 Fax: 831 459 3383 email: [email protected] http://bio.research.ucsc.edu/people/bernardi _______________________________________________ R-sig-phylo mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
