COTree, developed in Dr. Mullins' lab at University of Washington, is a web interface to re-root a phylogenetic tree at the least squares point (Center Of the Tree). COT and its applications to HIV vaccine design are explained at length in the following references:
Example for newick tree with branch lengths:
((((((((((((a:0.00612000,b:0.00595500):0.01387200,c:0.01541200):0.01137700,((d:0.00893100,e:0.00854900):0.00682500,f:0.00684900):0.00199800):0.00000000,((g:0.02244900,((h:0.00345900,i:0.00515800):0.00706400,(j:0.00169600,k:0.00342400):0.00164900):0.00427000):0.00169100,l:0.01615600):0.00462800):0.00199400,(m:0.01245800,n:0.01418600):0.00353400):0.01074400,o:0.01140200):0.00864400,(p:0.00000000,q:0.00168400):0.01595200):0.01238600,(r:0.01226800,s:0.01613900):0.00124300):0.00201200,(t:0.05447700,u:0.01046900):0.00444700):0.05659400,OG1:0.12043000):0.04544800,og2:0.16630300):0.04016250,(og3:0.18159100,og4:0.11105600):0.02776250);
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