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example output from running the RAG-1 dataset of Waddell et al. We ne…

…ed to make a table or figure of the points that are directly comprable to the "Expected" column of Waddell et al.
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1 parent d61b590 commit e44ba6ba4782e09297f18f17288735f377e94b03 @mtholder committed Aug 20, 2012
Showing with 334 additions and 0 deletions.
  1. +334 −0 test/waddellEtAl/rag1wMLTreeOutput.txt
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+COMMAND:
+ ../../src/PhyPatClassProb -f0.252818,0.284001,0.256973 -r1.86149,5.25704,0.72040,0.97137,6.83511 ./rag1wMLTree.nex -m0,0.129385382,0.348650344,0.57517613,0.831849857,1.14122287,1.54443828,2.148571055,3.696423412 -p0.23193,0.09600875,0.09600875,0.09600875,0.09600875,0.09600875,0.09600875,0.09600875 2>/dev/null >>rag1wMLTreeOutput.txt
+argc = 6
+argv[0] = ../../src/PhyPatClassProb
+argv[1] = -f0.252818,0.284001,0.256973
+Expected steps = 0 states = A prob = 0.0985817
+Expected steps = 0 states = C prob = 0.108919
+Expected steps = 0 states = G prob = 0.104594
+Expected steps = 0 states = T prob = 0.0758656
+Expected steps = 1 states = AC prob = 0.0191182
+Expected steps = 1 states = AG prob = 0.0553001
+Expected steps = 1 states = CG prob = 0.0114706
+Expected steps = 1 states = AT prob = 0.00518041
+Expected steps = 1 states = CT prob = 0.0504409
+Expected steps = 1 states = GT prob = 0.00780708
+Expected steps = 2 states = AC prob = 0.00371025
+Expected steps = 2 states = AG prob = 0.0302267
+Expected steps = 2 states = CG prob = 0.00130146
+Expected steps = 2 states = ACG prob = 0.0201481
+Expected steps = 2 states = AT prob = 0.000346174
+Expected steps = 2 states = CT prob = 0.0302755
+Expected steps = 2 states = ACT prob = 0.0146642
+Expected steps = 2 states = GT prob = 0.000708772
+Expected steps = 2 states = AGT prob = 0.00910903
+Expected steps = 2 states = CGT prob = 0.0112263
+Expected steps = 3 states = AC prob = 0.000681465
+Expected steps = 3 states = AG prob = 0.0155032
+Expected steps = 3 states = CG prob = 0.000143836
+Expected steps = 3 states = ACG prob = 0.0196355
+Expected steps = 3 states = AT prob = 2.28714e-05
+Expected steps = 3 states = CT prob = 0.0173768
+Expected steps = 3 states = ACT prob = 0.0145152
+Expected steps = 3 states = GT prob = 6.14509e-05
+Expected steps = 3 states = AGT prob = 0.00799148
+Expected steps = 3 states = CGT prob = 0.0105073
+Expected steps = 3 states = ACGT prob = 0.00871564
+Expected steps = 4 states = AC prob = 0.000119282
+Expected steps = 4 states = AG prob = 0.00753713
+Expected steps = 4 states = CG prob = 1.56895e-05
+Expected steps = 4 states = ACG prob = 0.0153256
+Expected steps = 4 states = AT prob = 1.50828e-06
+Expected steps = 4 states = CT prob = 0.0095625
+Expected steps = 4 states = ACT prob = 0.0116123
+Expected steps = 4 states = GT prob = 5.14194e-06
+Expected steps = 4 states = AGT prob = 0.00578834
+Expected steps = 4 states = CGT prob = 0.00834499
+Expected steps = 4 states = ACGT prob = 0.0137442
+Expected steps = 5 states = AC prob = 2.01672e-05
+Expected steps = 5 states = AG prob = 0.00352378
+Expected steps = 5 states = CG prob = 1.7179e-06
+Expected steps = 5 states = ACG prob = 0.0109653
+Expected steps = 5 states = AT prob = 1.0119e-07
+Expected steps = 5 states = CT prob = 0.00508343
+Expected steps = 5 states = ACT prob = 0.00851038
+Expected steps = 5 states = GT prob = 4.21561e-07
+Expected steps = 5 states = AGT prob = 0.00383823
+Expected steps = 5 states = CGT prob = 0.00615461
+Expected steps = 5 states = ACGT prob = 0.0155905
+Expected steps = 6 states = AC prob = 3.32914e-06
+Expected steps = 6 states = AG prob = 0.00159528
+Expected steps = 6 states = CG prob = 1.88163e-07
+Expected steps = 6 states = ACG prob = 0.00746713
+Expected steps = 6 states = AT prob = 6.97332e-09
+Expected steps = 6 states = CT prob = 0.00263566
+Expected steps = 6 states = ACT prob = 0.00594442
+Expected steps = 6 states = GT prob = 3.41256e-08
+Expected steps = 6 states = AGT prob = 0.00239822
+Expected steps = 6 states = CGT prob = 0.00433384
+Expected steps = 6 states = ACGT prob = 0.0154759
+Expected steps = 7 states = AC prob = 5.32478e-07
+Expected steps = 7 states = AG prob = 0.000689639
+Expected steps = 7 states = CG prob = 1.98561e-08
+Expected steps = 7 states = ACG prob = 0.00484284
+Expected steps = 7 states = AT prob = 4.81496e-10
+Expected steps = 7 states = CT prob = 0.00133519
+Expected steps = 7 states = ACT prob = 0.00400366
+Expected steps = 7 states = GT prob = 2.69114e-09
+Expected steps = 7 states = AGT prob = 0.00140547
+Expected steps = 7 states = CGT prob = 0.00294355
+Expected steps = 7 states = ACGT prob = 0.0141212
+Expected steps = 8 states = AC prob = 7.99758e-08
+Expected steps = 8 states = AG prob = 0.000275173
+Expected steps = 8 states = CG prob = 1.91283e-09
+Expected steps = 8 states = ACG prob = 0.00291993
+Expected steps = 8 states = AT prob = 3.15338e-11
+Expected steps = 8 states = CT prob = 0.000649579
+Expected steps = 8 states = ACT prob = 0.00256323
+Expected steps = 8 states = GT prob = 1.99757e-10
+Expected steps = 8 states = AGT prob = 0.000751499
+Expected steps = 8 states = CGT prob = 0.0019043
+Expected steps = 8 states = ACGT prob = 0.0118244
+Expected steps = 9 states = AC prob = 1.08122e-08
+Expected steps = 9 states = AG prob = 9.73843e-05
+Expected steps = 9 states = CG prob = 1.60626e-10
+Expected steps = 9 states = ACG prob = 0.00158586
+Expected steps = 9 states = AT prob = 1.85111e-12
+Expected steps = 9 states = CT prob = 0.000292748
+Expected steps = 9 states = ACT prob = 0.00151184
+Expected steps = 9 states = GT prob = 1.33918e-11
+Expected steps = 9 states = AGT prob = 0.000354876
+Expected steps = 9 states = CGT prob = 0.00113809
+Expected steps = 9 states = ACGT prob = 0.00890506
+Expected steps = 10 states = AC prob = 1.26555e-09
+Expected steps = 10 states = AG prob = 2.95266e-05
+Expected steps = 10 states = CG prob = 1.13882e-11
+Expected steps = 10 states = ACG prob = 0.000755944
+Expected steps = 10 states = AT prob = 9.33725e-14
+Expected steps = 10 states = CT prob = 0.000117074
+Expected steps = 10 states = ACT prob = 0.000794492
+Expected steps = 10 states = GT prob = 7.81663e-13
+Expected steps = 10 states = AGT prob = 0.00014422
+Expected steps = 10 states = CGT prob = 0.000606867
+Expected steps = 10 states = ACGT prob = 0.00591116
+Expected steps = 11 states = AC prob = 1.24292e-10
+Expected steps = 11 states = AG prob = 7.45595e-06
+Expected steps = 11 states = CG prob = 6.66347e-13
+Expected steps = 11 states = ACG prob = 0.000310774
+Expected steps = 11 states = AT prob = 3.92792e-15
+Expected steps = 11 states = CT prob = 3.99125e-05
+Expected steps = 11 states = ACT prob = 0.000361987
+Expected steps = 11 states = GT prob = 3.85416e-14
+Expected steps = 11 states = AGT prob = 4.95408e-05
+Expected steps = 11 states = CGT prob = 0.000280342
+Expected steps = 11 states = ACGT prob = 0.00340939
+Expected steps = 12 states = AC prob = 9.96632e-12
+Expected steps = 12 states = AG prob = 1.52781e-06
+Expected steps = 12 states = CG prob = 3.15149e-14
+Expected steps = 12 states = ACG prob = 0.000108918
+Expected steps = 12 states = AT prob = 1.34376e-16
+Expected steps = 12 states = CT prob = 1.11895e-05
+Expected steps = 12 states = ACT prob = 0.000140031
+Expected steps = 12 states = GT prob = 1.56186e-15
+Expected steps = 12 states = AGT prob = 1.41921e-05
+Expected steps = 12 states = CGT prob = 0.000109645
+Expected steps = 12 states = ACGT prob = 0.0016928
+Expected steps = 13 states = AC prob = 6.33831e-13
+Expected steps = 13 states = AG prob = 2.46807e-07
+Expected steps = 13 states = CG prob = 1.17533e-15
+Expected steps = 13 states = ACG prob = 3.22525e-05
+Expected steps = 13 states = AT prob = 3.63691e-18
+Expected steps = 13 states = CT prob = 2.48854e-06
+Expected steps = 13 states = ACT prob = 4.51872e-05
+Expected steps = 13 states = GT prob = 5.04875e-17
+Expected steps = 13 states = AGT prob = 3.34824e-06
+Expected steps = 13 states = CGT prob = 3.56151e-05
+Expected steps = 13 states = ACGT prob = 0.000718602
+Expected steps = 14 states = AC prob = 3.08353e-14
+Expected steps = 14 states = AG prob = 3.02987e-08
+Expected steps = 14 states = CG prob = 3.34193e-17
+Expected steps = 14 states = ACG prob = 7.99824e-06
+Expected steps = 14 states = AT prob = 7.51477e-20
+Expected steps = 14 states = CT prob = 4.21227e-07
+Expected steps = 14 states = ACT prob = 1.19549e-05
+Expected steps = 14 states = GT prob = 1.25411e-18
+Expected steps = 14 states = AGT prob = 6.41328e-07
+Expected steps = 14 states = CGT prob = 9.42972e-06
+Expected steps = 14 states = ACGT prob = 0.000259143
+Expected steps = 15 states = AC prob = 1.09252e-15
+Expected steps = 15 states = AG prob = 2.68977e-09
+Expected steps = 15 states = CG prob = 6.9064e-19
+Expected steps = 15 states = ACG prob = 1.64393e-06
+Expected steps = 15 states = AT prob = 1.12833e-21
+Expected steps = 15 states = CT prob = 5.14738e-08
+Expected steps = 15 states = ACT prob = 2.54474e-06
+Expected steps = 15 states = GT prob = 2.27633e-20
+Expected steps = 15 states = AGT prob = 9.80031e-08
+Expected steps = 15 states = CGT prob = 1.9939e-06
+Expected steps = 15 states = ACGT prob = 7.88195e-05
+Expected steps = 16 states = AC prob = 2.6293e-17
+Expected steps = 16 states = AG prob = 1.61034e-10
+Expected steps = 16 states = CG prob = 9.67868e-21
+Expected steps = 16 states = ACG prob = 2.76415e-07
+Expected steps = 16 states = AT prob = 1.14709e-23
+Expected steps = 16 states = CT prob = 4.226e-09
+Expected steps = 16 states = ACT prob = 4.26742e-07
+Expected steps = 16 states = GT prob = 2.81219e-22
+Expected steps = 16 states = AGT prob = 1.16951e-08
+Expected steps = 16 states = CGT prob = 3.28945e-07
+Expected steps = 16 states = ACGT prob = 2.00496e-05
+Expected steps = 17 states = AC prob = 3.8692e-19
+Expected steps = 17 states = AG prob = 5.85681e-12
+Expected steps = 17 states = CG prob = 8.27751e-23
+Expected steps = 17 states = ACG prob = 3.73929e-08
+Expected steps = 17 states = AT prob = 7.09415e-26
+Expected steps = 17 states = CT prob = 2.09765e-10
+Expected steps = 17 states = ACT prob = 5.50874e-08
+Expected steps = 17 states = GT prob = 2.12535e-24
+Expected steps = 17 states = AGT prob = 1.06249e-09
+Expected steps = 17 states = CGT prob = 4.12276e-08
+Expected steps = 17 states = ACGT prob = 4.22395e-06
+Expected steps = 18 states = AC prob = 2.91458e-21
+Expected steps = 18 states = AG prob = 1.08536e-13
+Expected steps = 18 states = CG prob = 3.61125e-25
+Expected steps = 18 states = ACG prob = 3.98417e-09
+Expected steps = 18 states = AT prob = 2.22514e-28
+Expected steps = 18 states = CT prob = 5.28717e-12
+Expected steps = 18 states = ACT prob = 5.3391e-09
+Expected steps = 18 states = GT prob = 8.20536e-27
+Expected steps = 18 states = AGT prob = 7.13515e-11
+Expected steps = 18 states = CGT prob = 3.80892e-09
+Expected steps = 18 states = ACGT prob = 7.28981e-07
+Expected steps = 19 states = AC prob = 7.78528e-24
+Expected steps = 19 states = AG prob = 7.14268e-16
+Expected steps = 19 states = CG prob = 5.53662e-28
+Expected steps = 19 states = ACG prob = 3.25403e-10
+Expected steps = 19 states = AT prob = 2.42444e-31
+Expected steps = 19 states = CT prob = 4.7689e-14
+Expected steps = 19 states = ACT prob = 3.78278e-10
+Expected steps = 19 states = GT prob = 1.11482e-29
+Expected steps = 19 states = AGT prob = 3.42411e-12
+Expected steps = 19 states = CGT prob = 2.50687e-10
+Expected steps = 19 states = ACGT prob = 1.01807e-07
+Expected steps = 20 states = AC prob = 2.53782e-27
+Expected steps = 20 states = AG prob = 5.89871e-19
+Expected steps = 20 states = CG prob = 1.00571e-31
+Expected steps = 20 states = ACG prob = 1.96723e-11
+Expected steps = 20 states = AT prob = 3.04247e-35
+Expected steps = 20 states = CT prob = 5.57758e-17
+Expected steps = 20 states = ACT prob = 1.90251e-11
+Expected steps = 20 states = GT prob = 1.80606e-33
+Expected steps = 20 states = AGT prob = 1.12927e-13
+Expected steps = 20 states = CGT prob = 1.13021e-11
+Expected steps = 20 states = ACGT prob = 1.13446e-08
+Expected steps = 21 states = AC prob = 0
+Expected steps = 21 states = AG prob = 0
+Expected steps = 21 states = CG prob = 0
+Expected steps = 21 states = ACG prob = 8.40747e-13
+Expected steps = 21 states = AT prob = 0
+Expected steps = 21 states = CT prob = 0
+Expected steps = 21 states = ACT prob = 6.55928e-13
+Expected steps = 21 states = GT prob = 0
+Expected steps = 21 states = AGT prob = 2.44448e-15
+Expected steps = 21 states = CGT prob = 3.33352e-13
+Expected steps = 21 states = ACGT prob = 9.91591e-10
+Expected steps = 22 states = AC prob = 0
+Expected steps = 22 states = AG prob = 0
+Expected steps = 22 states = CG prob = 0
+Expected steps = 22 states = ACG prob = 2.38602e-14
+Expected steps = 22 states = AT prob = 0
+Expected steps = 22 states = CT prob = 0
+Expected steps = 22 states = ACT prob = 1.47825e-14
+Expected steps = 22 states = GT prob = 0
+Expected steps = 22 states = AGT prob = 3.28143e-17
+Expected steps = 22 states = CGT prob = 6.07813e-15
+Expected steps = 22 states = ACGT prob = 6.65129e-11
+Expected steps = 23 states = AC prob = 0
+Expected steps = 23 states = AG prob = 0
+Expected steps = 23 states = CG prob = 0
+Expected steps = 23 states = ACG prob = 4.11174e-16
+Expected steps = 23 states = AT prob = 0
+Expected steps = 23 states = CT prob = 0
+Expected steps = 23 states = ACT prob = 2.02087e-16
+Expected steps = 23 states = GT prob = 0
+Expected steps = 23 states = AGT prob = 2.52788e-19
+Expected steps = 23 states = CGT prob = 6.34307e-17
+Expected steps = 23 states = ACGT prob = 3.32504e-12
+Expected steps = 24 states = AC prob = 0
+Expected steps = 24 states = AG prob = 0
+Expected steps = 24 states = CG prob = 0
+Expected steps = 24 states = ACG prob = 3.75102e-18
+Expected steps = 24 states = AT prob = 0
+Expected steps = 24 states = CT prob = 0
+Expected steps = 24 states = ACT prob = 1.47365e-18
+Expected steps = 24 states = GT prob = 0
+Expected steps = 24 states = AGT prob = 9.88195e-22
+Expected steps = 24 states = CGT prob = 3.35469e-19
+Expected steps = 24 states = ACGT prob = 1.19003e-13
+Expected steps = 25 states = AC prob = 0
+Expected steps = 25 states = AG prob = 0
+Expected steps = 25 states = CG prob = 0
+Expected steps = 25 states = ACG prob = 1.43415e-20
+Expected steps = 25 states = AT prob = 0
+Expected steps = 25 states = CT prob = 0
+Expected steps = 25 states = ACT prob = 4.5348e-21
+Expected steps = 25 states = GT prob = 0
+Expected steps = 25 states = AGT prob = 1.56625e-24
+Expected steps = 25 states = CGT prob = 7.20085e-22
+Expected steps = 25 states = ACGT prob = 2.88248e-15
+Expected steps = 26 states = AC prob = 0
+Expected steps = 26 states = AG prob = 0
+Expected steps = 26 states = CG prob = 0
+Expected steps = 26 states = ACG prob = 1.35969e-23
+Expected steps = 26 states = AT prob = 0
+Expected steps = 26 states = CT prob = 0
+Expected steps = 26 states = ACT prob = 3.42931e-24
+Expected steps = 26 states = GT prob = 0
+Expected steps = 26 states = AGT prob = 5.74929e-28
+Expected steps = 26 states = CGT prob = 3.58782e-25
+Expected steps = 26 states = ACGT prob = 4.35852e-17
+Expected steps = 27 states = AC prob = 0
+Expected steps = 27 states = AG prob = 0
+Expected steps = 27 states = CG prob = 0
+Expected steps = 27 states = ACG prob = 0
+Expected steps = 27 states = AT prob = 0
+Expected steps = 27 states = CT prob = 0
+Expected steps = 27 states = ACT prob = 0
+Expected steps = 27 states = GT prob = 0
+Expected steps = 27 states = AGT prob = 0
+Expected steps = 27 states = CGT prob = 0
+Expected steps = 27 states = ACGT prob = 3.64113e-19
+Expected steps = 28 states = AC prob = 0
+Expected steps = 28 states = AG prob = 0
+Expected steps = 28 states = CG prob = 0
+Expected steps = 28 states = ACG prob = 0
+Expected steps = 28 states = AT prob = 0
+Expected steps = 28 states = CT prob = 0
+Expected steps = 28 states = ACT prob = 0
+Expected steps = 28 states = GT prob = 0
+Expected steps = 28 states = AGT prob = 0
+Expected steps = 28 states = CGT prob = 0
+Expected steps = 28 states = ACGT prob = 1.36404e-21
+Expected steps = 29 states = AC prob = 0
+Expected steps = 29 states = AG prob = 0
+Expected steps = 29 states = CG prob = 0
+Expected steps = 29 states = ACG prob = 0
+Expected steps = 29 states = AT prob = 0
+Expected steps = 29 states = CT prob = 0
+Expected steps = 29 states = ACT prob = 0
+Expected steps = 29 states = GT prob = 0
+Expected steps = 29 states = AGT prob = 0
+Expected steps = 29 states = CGT prob = 0
+Expected steps = 29 states = ACGT prob = 1.42479e-24
+Expected steps = 30 states = AC prob = 0
+Expected steps = 30 states = AG prob = 0
+Expected steps = 30 states = CG prob = 0
+Expected steps = 30 states = ACG prob = 0
+Expected steps = 30 states = AT prob = 0
+Expected steps = 30 states = CT prob = 0
+Expected steps = 30 states = ACT prob = 0
+Expected steps = 30 states = GT prob = 0
+Expected steps = 30 states = AGT prob = 0
+Expected steps = 30 states = CGT prob = 0
+Expected steps = 30 states = ACGT prob = 5.43617e-29
+totalprob = 1

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