# mutates a sequence according to the Jukes-Cantor model
# X is an numpy.array with entries in {0,1,2,3}
# t is branch length
# mu is mutation rate
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def mutate(X,t,mu):
import numpy.random as rand
mutatedSeq = X.copy()
numMutation = rand.poisson(L*mu*t)
for i in range(numMutation):
site = rand.randint(0,L)
mutatedSeq[site] = rand.randint(0,4)
return mutatedSeq
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