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张东
Jun 29, 2019, 9:15:40 PM6/29/19
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Dear all,
I have two different topologies generated from 28S (tree-28S) and mitogenome (tree-MT), respectively, and I tried to conduct AU test on them using both datasets. The results (as shown below) showed that the tree-MT was rejected in the AU test using 28S dataset (28S AU test), whereas the tree-28S was rejected in the AU test using MT dataset (MT AU test). Therefore, I wanna to know how AU test compare the topologies? Does it first selects a tree with highest logL, and then compares each of the user trees to this tree? If take the my results (below) as example, I am comparing tree-MT to tree-28S in 28S AU test, and comparing tree-28S to tree-MT in MT AU test.
If I am wrong, what is tree-28S comparing to in 28S AU test? and what is tree-MT comparing to in MT AU test?
AU test based on 28S dataset (iqtree -s 28S.phy -m GTR+G -z trees.treels -n 0 -zb 10000 -au).
Tree logL deltaL bp-RELL p-KH p-SH c-ELW p-AU
-------------------------------------------------------------------------
MT -22822.25152 30.811 0.0005 - 0.001 - 0.001 - 0.000702 - 0.000633 -
28S -22791.44054 0 1 + 0.999 + 1 + 0.999 + 0.999 +
AU test based on mitochondrial genome dataset (iqtree -s mitogenome.phy -m mtZOA+F+I+G4 -z trees.treels -n 0 -zb 10000 -au).
Tree logL deltaL bp-RELL p-KH p-SH c-ELW p-AU
-------------------------------------------------------------------------
MT -54731.89675 0 1 + 1 + 1 + 1 + 1 +
28S -59255.35408 4523.5 0 - 0 - 0 - 0 - 4.61e-05 -
Thank you for your help!
Minh Bui
Jun 30, 2019, 3:47:11 PM6/30/19
to IQ-TREE, 张东
Hi there,
Heiko can better answer your question. I suggest that you have a look at his book chapter on Tree Topology Tests in "The Phylogenetic Handbook: A practical approach to phylogenetic analysis and hypothesis testing”:
This provides a much better explanation than the original Shimodaira’s paper.
Cheers,
Minh
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张东
Jun 30, 2019, 9:59:04 PM6/30/19
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Hi Minh,
在 2019年7月1日星期一 UTC+8上午3:47:11，Minh Bui写道：
Thank you for your help. I am going to look into that book chapter.
Sincerely,
Dong Zhang
在 2019年7月1日星期一 UTC+8上午3:47:11，Minh Bui写道：
Hi there,Heiko can better answer your question. I suggest that you have a look at his book chapter on Tree Topology Tests in "The Phylogenetic Handbook: A practical approach to phylogenetic analysis and hypothesis testing”:
This provides a much better explanation than the original Shimodaira’s paper.Cheers,Minh
On 30 Jun 2019, at 11:15 am, 张东 <dongzh...@gmail.com> wrote:
Dear all,I have two different topologies generated from 28S (tree-28S) and mitogenome (tree-MT), respectively, and I tried to conduct AU test on them using both datasets. The results (as shown below) showed that the tree-MT was rejected in the AU test using 28S dataset (28S AU test), whereas the tree-28S was rejected in the AU test using MT dataset (MT AU test). Therefore, I wanna to know how AU test compare the topologies? Does it first selects a tree with highest logL, and then compares each of the user trees to this tree? If take the my results (below) as example, I am comparing tree-MT to tree-28S in 28S AU test, and comparing tree-28S to tree-MT in MT AU test.If I am wrong, what is tree-28S comparing to in 28S AU test? and what is tree-MT comparing to in MT AU test?AU test based on 28S dataset (iqtree -s 28S.phy -m GTR+G -z trees.treels -n 0 -zb 10000 -au).Tree logL deltaL bp-RELL p-KH p-SH c-ELW p-AU-------------------------------------------------------------------------MT -22822.25152 30.811 0.0005 - 0.001 - 0.001 - 0.000702 - 0.000633 -28S -22791.44054 0 1 + 0.999 + 1 + 0.999 + 0.999 +AU test based on mitochondrial genome dataset (iqtree -s mitogenome.phy -m mtZOA+F+I+G4 -z trees.treels -n 0 -zb 10000 -au).Tree logL deltaL bp-RELL p-KH p-SH c-ELW p-AU-------------------------------------------------------------------------MT -54731.89675 0 1 + 1 + 1 + 1 + 1 +28S -59255.35408 4523.5 0 - 0 - 0 - 0 - 4.61e-05 -Thank you for your help!--
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