tbigot/tpms — Issue #8: missed root in tpms_computations RU
Author: flassalle
Created: 2012-01-18 14:43:42+00:00
State: open

One case where the output of RU is not (one of) the root giving the minimal sum of unicity scores.

here is the original tree (as in tree database formated by tpms_mkdb):

HBG001548.phb
[
ATU7B_1_SLYA"ATU7B"
ATU7C_1_SLYA"ATU7C"
ATU7A_1_SLYA"ATU7A"
ATU13_1_SLYA"ATU13"
ATU5A_1_SLYA"ATU5A"
ATU2A_1_SLYA"ATU2A"
ATU4C_1_SLYA"ATU4C"
ATU4B_1_SLYA"ATU4B"
ATU4A_1_SLYA"ATU4A"
ATU9A_1_SLYA"ATU9A"
ATU1C_1_SLYA"ATU1C"
ATU1B_1_SLYA"ATU1B"
ATU1A_1_SLYA"ATU1A"
ATU8A_1_SLYA"ATU8A"
AGRT5_1_PE1067"AGRT5"
ATU3A_1_SLYA"ATU3A"
ATU6A_1_SLYA"ATU6A"
AGRRK_1_PE1234"AGRRK"
SINMW_1_PE731"SINMW"
SIMEL1_2_PE1136"SIMEL1"
ATU1C_3_PE463"ATU1C"
AGRVS_2_PE568"AGRVS"
AGRRK_1_PE1507"AGRRK"
ATU4A_1_PE3006"ATU4A"
]
(((((((((((ATU7B_1_SLYA:1e-10,ATU7C_1_SLYA:0.0153245733)0.0:4.515e-07,ATU7A_1_SLYA:1e-10)0.0:9.03e-07,((ATU13_1_SLYA:1e-10,ATU5A_1_SLYA:1e-10)0.755:0.0077356816,ATU2A_1_SLYA:0.0154178072)0.759:0.0075908841)0.0:5.02e-07,((ATU4C_1_SLYA:1e-10,ATU4B_1_SLYA:1e-10)0.856:0.0076550764,ATU4A_1_SLYA:5.273e-07)0.836:0.0155106944)0.778:0.0102347771,ATU9A_1_SLYA:0.0053604199)0.855:0.0154048532,(ATU1C_1_SLYA:1e-10,(ATU1B_1_SLYA:1e-10,ATU1A_1_SLYA:1e-10)0.0:1e-10)0.886:0.0155730925)0.433:0.0095589268,((ATU8A_1_SLYA:0.0077396087,(AGRT5_1_PE1067:7.681e-07,ATU3A_1_SLYA:0.0077792728)0.0:5.88e-07)0.0:5.325e-07,ATU6A_1_SLYA:0.0156634547)0.745:0.0142423688)0.999:0.4409643582,AGRRK_1_PE1234:0.3312947792):0.1093171772,(SINMW_1_PE731:0.0740601495,SIMEL1_2_PE1136:0.0387884966):0.2577709492)0.685:0.1878338621,ATU1C_3_PE463:1.1638138625):0.0478866248,((AGRVS_2_PE568:0.2993867508,AGRRK_1_PE1507:0.2774220742):0.4824473097,ATU4A_1_PE3006:0.9582788272):0.9996290192)0.931:0;

and here is the output after running RU followed by AU programs:

(([0]AGRRK_1_PE1234:0.331295,(([0]SINMW_1_PE731:0.0740601,[0]SIMEL1_2_PE1136:0.0387885)[0]:0.257771,([0]ATU1C_3_PE463:1.16381,(([0]AGRVS_2_PE568:0.299387,[0]AGRRK_1_PE1507:0.277422)[0]:0.482447,[0]ATU4A_1_PE3006:0.958279)[0]:1.04752)[0]:0.187834)[0]0.685:0.109317)[0.693147]:0.220482,((((((([0]ATU7B_1_SLYA:1e-10,[0]ATU7C_1_SLYA:0.0153246)[0]0.0:4.515e-07,[0]ATU7A_1_SLYA:1e-10)[0]0.0:9.03e-07,(([0]ATU13_1_SLYA:1e-10,[0]ATU5A_1_SLYA:1e-10)[0]0.755:0.00773568,[0]ATU2A_1_SLYA:0.0154178)[0]0.759:0.00759088)[0]0.0:5.02e-07,(([0]ATU4C_1_SLYA:1e-10,[0]ATU4B_1_SLYA:1e-10)[0]0.856:0.00765508,[0]ATU4A_1_SLYA:5.273e-07)[0]0.836:0.0155107)[0]0.778:0.0102348,[0]ATU9A_1_SLYA:0.00536042)[0]0.855:0.0154049,([0]ATU1C_1_SLYA:1e-10,([0]ATU1B_1_SLYA:1e-10,[0]ATU1A_1_SLYA:1e-10)[0]0.0:1e-10)[0]0.886:0.0155731)[0]0.433:0.00955893,(([0]ATU8A_1_SLYA:0.00773961,([0]AGRT5_1_PE1067:7.681e-07,[0]ATU3A_1_SLYA:0.00777927)[0]0.0:5.88e-07)[0]0.0:5.325e-07,[0]ATU6A_1_SLYA:0.0156635)[0]0.745:0.0142424)[0]0.999:0.220482)[2.07944];

while the minimum-sum-of-unity-scores tree is the following:

((((((((((ATU7B_1_SLYA:1.0E-10,ATU7C_1_SLYA:0.0153245733)0.0:4.515E-7,ATU7A_1_SLYA:1.0E-10)0.0:9.03E-7,((ATU13_1_SLYA:1.0E-10,ATU5A_1_SLYA:1.0E-10)0.755:0.0077356816,ATU2A_1_SLYA:0.0154178072)0.759:0.0075908841)0.0:5.02E-7,((ATU4C_1_SLYA:1.0E-10,ATU4B_1_SLYA:1.0E-10)0.856:0.0076550764,ATU4A_1_SLYA:5.273E-7)0.836:0.0155106944)0.778:0.0102347771,ATU9A_1_SLYA:0.0053604199)0.855:0.0154048532,(ATU1C_1_SLYA:1.0E-10,(ATU1B_1_SLYA:1.0E-10,ATU1A_1_SLYA:1.0E-10)0.0:1.0E-10)0.886:0.0155730925)0.433:0.0095589268,((ATU8A_1_SLYA:0.0077396087,(AGRT5_1_PE1067:7.681E-7,ATU3A_1_SLYA:0.0077792728)0.0:5.88E-7)0.0:5.325E-7,ATU6A_1_SLYA:0.0156634547)0.745:0.0142423688)0.999:0.4409643582,AGRRK_1_PE1234:0.3312947792):0.1093171772,(SINMW_1_PE731:0.0740601495,SIMEL1_2_PE1136:0.0387884966):0.2577709492)0.685:0.09391693105,(((AGRVS_2_PE568:0.2993867508,AGRRK_1_PE1507:0.2774220742):0.4824473097,ATU4A_1_PE3006:0.9582788272):1.047515644,ATU1C_3_PE463:1.1638138625):0.09391693105);

I cannot see what is the problem with the input tree that could lead tpms to overlook this solution....