# Another example file
SequenceLen = 29
SequenceNum = 5
OutputFilename = "outfile"
InputType = 4 /* DNA */
TheAlphabet = "ACGT"
TheFreq = [.25,.25,.25,.25]
Relatedness = 1
NumberOfRuns = 1
ChooseFromLeaves = True
TheSequence = "AGTCTGTACTATAATGGGAGGAAAGCCGA"
TheTree = ((a:3,b:5):5,(c:4,d:2,e:4):5,(f:3,g:4):6,(h:3,i:3):4,j:5);
TheMutationProbability = [1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0]

TheInsertThreshold = 0.002
TheDeleteThreshold = 0.002

TheInsFunc = [.2,.2,.2,1,1,1,1]
TheDelFunc = [.2,.2,.2,1,1,1,1]

ThePAMMatrix = [[.97,.01,.01,.01],
                [.01,.97,.01,.01],
                [.01,.01,.97,.01],
                [.01,.01,.01,.97]]