AU test discrepancy

[ARP]

HI Minh,

 

I am trying (IQ-TREE v1.5.6) to use the AU test with mixture models, but I have obtained significant different p-AU values (e.g., trees #1 and #8 highlighted in yellow) for some trees just after scrambling the order of my trees in the input file: same trees, same alignment, same model and same logL values as you can see in the output table. The best tree is consistently the same (tree# 13; green highlight)

Do you have an idea what the problem is?

 

These are the results after two runs (I edited the name of the trees just to show them with the same IDs):

 

Run 1

 

Tree      logL    deltaL  bp-RELL    p-KH     p-SH    p-WKH    p-WSH    c-ELW     p-AU

-------------------------------------------------------------------------------------------

  1  -518214.988 1108.235  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.2023 + 

  2  -518454.608 1347.855  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 

  3  -518249.770 1143.017  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0021 - 

  4  -518640.277 1533.524  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0030 - 

  5  -517816.275 709.522  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 

  6  -517681.152 574.399  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0071 - 

  7  -517684.603 577.850  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0001 - 

  8  -517335.076 228.323  0.0000 - 0.0000 - 0.0080 - 0.0000 - 0.0000 - 0.0000 - 0.0053 - 

  9  -517297.225 190.472  0.0000 - 0.0000 - 0.0230 - 0.0000 - 0.0000 - 0.0000 - 0.0198 - 

 10  -517277.698 170.945  0.0000 - 0.0000 - 0.0360 - 0.0000 - 0.0000 - 0.0000 - 0.0005 - 

 11  -517142.644  35.891  0.0010 - 0.0050 - 0.7640 + 0.0050 - 0.0410 - 0.0012 - 0.0040 - 

 12  -517132.212  25.459  0.0520 + 0.0460 - 0.8470 + 0.0460 - 0.3030 + 0.0521 + 0.0452 - 

 13  -517106.753   0.000  0.9470 + 0.9540 + 1.0000 + 0.9540 + 1.0000 + 0.9467 + 0.9631 + 

Run 2

Tree      logL    deltaL  bp-RELL    p-KH     p-SH    p-WKH    p-WSH    c-ELW     p-AU

-------------------------------------------------------------------------------------------

 11  -517142.644  35.891  0.0010 - 0.0030 - 0.7770 + 0.0030 - 0.0280 - 0.0007 - 0.0213 - 

 12  -517132.212  25.459  0.0420 - 0.0450 - 0.8520 + 0.0450 - 0.2980 + 0.0451 - 0.0331 - 

 13  -517106.753   0.000  0.9570 + 0.9550 + 1.0000 + 0.9550 + 1.0000 + 0.9542 + 0.9706 + 

  1  -518214.988 1108.235  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0008 - 

  2  -518454.608 1347.855  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 

  3  -518249.770 1143.017  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0034 - 

  4  -518640.277 1533.524  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0043 - 

  5  -517816.275 709.522  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 

  6  -517681.152 574.399  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0214 - 

  7  -517684.603 577.850  0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 0.0000 - 

  8  -517335.076 228.323  0.0000 - 0.0000 - 0.0030 - 0.0000 - 0.0000 - 0.0000 - 0.2275 + 

  9  -517297.225 190.472  0.0000 - 0.0000 - 0.0170 - 0.0000 - 0.0000 - 0.0000 - 0.0280 - 

 10  -517277.698 170.945  0.0000 - 0.0000 - 0.0320 - 0.0000 - 0.0000 - 0.0000 - 0.0027 - 

Thank you for you help,

Adrian

[ARP]

Hi again Minh,

I forgot to say that the same problem occurs with Tree# 11.

Thank you for your help,

Adrian

[Bui Quang Minh]

Hi Adrian, can you pls send me the data set and command line via personal email? I will have a closer look.

Thanks, 

Minh 

Sent from my iPhone

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