mixture models and GUI

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Philipp Chetverikov

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Jul 7, 2019, 2:12:57 PM7/7/19
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1) Is it possible to ask IQ-tree (web version) to chose automatically mixture models for a partitioned multigene alignment (DNA+proteins) and get a tree?
2) Is it possible to dowload IQ-tree with the same GUI (as in the web page of IQ tree) and execute on a personal computer through this GUI?

张东

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Jul 7, 2019, 8:42:32 PM7/7/19
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Hi,

Regarding the second question, I have wrote a GUI that integrates the IQ-TREE, you can try it if you wish.


Dong

在 2019年7月8日星期一 UTC+8上午2:12:57,Philipp Chetverikov写道:

Minh Bui

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Jul 8, 2019, 5:04:12 AM7/8/19
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Hi Philipp, 

There is no way to just download iqtree web service and run it on a PC. But Dong gave an alternative solution PhyloSuite, which you might  have seen and it looks quite nice! So try it out. Moreover, Mesquite software also supports IQ-TREE. You can also try CIPRES server.

For your 1st question: to run mixed DNA+protein models, you need to run it from the command line (though I’m not sure if PhyloSuite supports that). There is a detailed guide how to set up such a run here: http://www.iqtree.org/doc/Complex-Models#partition-models

Cheers
Minh

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Philipp Chetverikov

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Jul 8, 2019, 11:23:40 AM7/8/19
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Hi, Dong,
thanks for the links. I will try PhyloSuite with pleasure and will be glad to cite it.
1) Does PhyloSuite have options for molecular clocks and calibration points? I did not find it in the tutorial
2) Does PhyloSuite allow to apply mixture models for a partitioned alignment?
Philipp

понедельник, 8 июля 2019 г., 3:42:32 UTC+3 пользователь 张东 написал:

Philipp Chetverikov

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Jul 8, 2019, 11:30:49 AM7/8/19
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Dear Minh,

thanks for the answer. What do you mean saying that "Mesquite software also supports IQ-TREE"? I use Mesquite to get a nexus file (fused multigene matrix) and upload this file to the IQtree web site (along with a partition file) for analysis. Could you suggest other options for using Mesquite and IQ-tree together?

Philipp

понедельник, 8 июля 2019 г., 12:04:12 UTC+3 пользователь Minh Bui написал:
Hi Philipp, 

There is no way to just download iqtree web service and run it on a PC. But Dong gave an alternative solution PhyloSuite, which you might  have seen and it looks quite nice! So try it out. Moreover, Mesquite software also supports IQ-TREE. You can also try CIPRES server.

For your 1st question: to run mixed DNA+protein models, you need to run it from the command line (though I’m not sure if PhyloSuite supports that). There is a detailed guide how to set up such a run here: http://www.iqtree.org/doc/Complex-Models#partition-models

Cheers
Minh
On 8 Jul 2019, at 10:42 am, 张东 <dongzh...@gmail.com> wrote:

Hi,

Regarding the second question, I have wrote a GUI that integrates the IQ-TREE, you can try it if you wish.


Dong

在 2019年7月8日星期一 UTC+8上午2:12:57,Philipp Chetverikov写道:


1) Is it possible to ask IQ-tree (web version) to chose automatically mixture models for a partitioned multigene alignment (DNA+proteins) and get a tree?
2) Is it possible to dowload IQ-tree with the same GUI (as in the web page of IQ tree) and execute on a personal computer through this GUI?

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Minh Bui

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Jul 8, 2019, 8:30:25 PM7/8/19
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Hi Philipp, CC David,

If you have used Mesquite, then you might be able to do all these analyses with it. You need to install a package called Zephyr: http://zephyr.mesquiteproject.org. It interacts with IQ-TREE (and other software) and automatically displays the tree once done, which is really cool.

I’m just not sure if this feature supports mixed DNA and protein data types.

@David: can you say if Zephyr supports mixed data matrix?

Cheers,
Minh

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张东

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Jul 9, 2019, 4:08:12 AM7/9/19
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Hi Philipp,

1. At the time, we haven't included these functions in the PhyloSuite.

2. As IQ-TREE is very versatile, we included only a part of its parameters in the PhyloSuite GUI. So this option is not included in the GUI. However, PhyloSuite offers an option for users to add parameters that are not included in the GUI. Just modify the preset command via the "View | Edit command" function in the dropdown arrow of the ‘Start’ button. In the screenshot below, I added this option by replacing '-m mtZOA+R6+F' with '-m "MIX{JC ,HKY}+G4"'. Then just click 'Save and run' button to start.

fig.png



Best regards,

Dong


在 2019年7月8日星期一 UTC+8下午11:23:40,Philipp Chetverikov写道:
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