the problem of parameters

[serene66]

Hi, I used the tree files provided in the paper ( QuartetScores -t 2 -r Mammalian_42taxa.reference.tre -e Mammalian_42taxa.evaluation.trees -o Mammalian_42taxa.scores ), but the result file I got is different from the one you provided. The result file I got has the information of these three parameters: [qp-ic:0.981790;lq-ic:0.951029;eqp-ic:0.971789]. Parameter [PIC:0.833,PICA:0.833,LIC:0.960,LICA:0.960, PP:1] is missing.

When I add the -q parameter ( QuartetScores -t 2 -r Mammalian_42taxa.reference.tre -e Mammalian_42taxa.evaluation.trees -o Mammalian_42taxa.scores -q Mammalian_42taxa.scores ) , I get the following error: PARSE ERROR: Argument: -q Couldn't find match for argument Brief USAGE: QuartetScores [-s] [-v] [-t ] -o -e -r [--] [--version] [-h]

Did I type the wrong command? How can I change it? Thank you very much!

[zhouxiaofan1983]

Hi,

QuartetScores only calculates the three flavors of quartet-based IC scores, namely lq-ic, qp-ic, and eqp-ic. The PIC/PICA/LIC/LICA values were bipartition-based IC scores calculated by RAxML, and the PP value was calculated by ASTRAL. These values were added to the output of QuartetScores afterward. Sorry for the confusion.

Best, Xiaofan

On Thu, Nov 4, 2021 at 4:21 PM serene66 @.***> wrote:

Hi, I used the tree files provided in the paper ( QuartetScores -t 2 -r Mammalian_42taxa.reference.tre -e Mammalian_42taxa.evaluation.trees -o Mammalian_42taxa.scores ), but the result file I got is different from the one you provided. The result file I got has the information of these three parameters: [qp-ic:0.981790;lq-ic:0.951029;eqp-ic:0.971789]. Parameter [PIC:0.833,PICA:0.833,LIC:0.960,LICA:0.960, PP:1] is missing.

When I add the -q parameter ( QuartetScores -t 2 -r Mammalian_42taxa.reference.tre -e Mammalian_42taxa.evaluation.trees -o Mammalian_42taxa.scores -q Mammalian_42taxa.scores ) , I get the following error: PARSE ERROR: Argument: -q Couldn't find match for argument Brief USAGE: QuartetScores [-s] [-v] [-t ] -o -e -r [--] [--version] [-h]

Did I type the wrong command? How can I change it? Thank you very much!

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[serene66]

Thank you. I have one more question. In my result, the EQP-IC is close to –1. Score values close to –1 suggest that the given internal branch is contested.“High LPP support values for internal branches with low IC scores would be reasonable if the incongruence is largely due to ILS; however, if the underlying cause(s) of incongruence are different, then the high LPP support values may be misleading.” If I get high PP and low EQP-IC [qp-ic:0.304648;lq-ic:0.251985;eqp-ic:-0.207884;PP:1.0], can I assume that ILS is play an important role? If not, what does that mean? I have used software Phylonet for hybridization detection, and there is no hybridization signal.