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from cogent import LoadTree, LoadSeqs
from cogent.draw import dendrogram
from cogent.evolve.models import GTR
import random


    

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pop = LoadTree("data/popn_tree.nwk")


    

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s = random.sample(pop.getTipNames(), 48)


    

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a = pop.getSubTree(s)


    

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a.scaleBranchLengths(1000)


    

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a.writeToFile('data/sample_tree.nwk', format='newick')


    

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model = GTR()


    

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lf = model.makeLikelihoodFunction(a)


    

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lf.setConstantLengths()


    

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aln = lf.simulateAlignment(100)


    

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