idvg developed in Dr. Mullins Lab at University of Washington is a web interface to assess a phylogenetic tree for evidence of continued viral replication during antiretroviral therapy. It inputs a newick tree with branch lengths, defined replication and non-replication sequences and number of random simulation testing, outputs the P value and id values of the test and random simulations.
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);
Example for replication file:
a
b
c
d
e
f
g
h
i
j
k
Example for non-replication file:
l
m
n
o
p