TreeMix plotting problem

[Hasini]

Hello everyone,
I used TreeMix program and built maximum likelihood tree, but when I rename some population names, the tree has changed (only positions of the populations have changed - a clade which held in the top now came to bottom and bottom clade transferred to top ).The result is almost same with the previous one only the position of clades has changed.
So now I'm looking for reasons. If someone knows the answer please give a quick response

[Vikram Chhatre]

You may want to post the before and after plots.  That might get you replies sooner.

In Treemix plots, divergence is measured on movement along X axis, not Y.  It sounds like your clades were just flipped, which may simply be a plotting issue.  

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[Hasini Wijayananda]

Dear Vikram
Thank you for the quick response.I have attached before and after plots in here. Plese check them and give me your suggestions.

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[Hasini Wijayananda]

On Monday, February 20, 2017 at 11:00:02 AM UTC+9, Hasini Wijayananda wrote:

Dear Vikram !
Thank you for the quick response.I have attached before and after plots here. In 2nd output I have renamed  4 abbriviations ( KPU as KPW, KDO as KDW, KNE as KJT, KHG as KJD)Plese check them and give me your suggestions.

[Vikram Chhatre]

Can you post high(er) resolution plots? 

On Sun, Feb 19, 2017 at 7:04 PM, Hasini Wijayananda <hasiniwi...@gmail.com> wrote:

On Monday, February 20, 2017 at 11:00:02 AM UTC+9, Hasini Wijayananda wrote:

Dear Vikram !
Thank you for the quick response.I have attached before and after plots here. In 2nd output I have renamed  4 abbriviations ( KPU as KPW, KDO as KDW, KNE as KJT, KHG as KJD)Plese check them and give me your suggestions.

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[Hasini Wijayananda]

Dear Vikram !

I have attached the higher dimension of previous plots.Please check them and give your suggestions.

Thank you!

[Vikram Chhatre]

There is no difference between these plots.  As I mentioned earlier, the divergence is measured by movement over x axis.  I see the same three migration routes in both plots and the approximate x positions of populations are the same despite flipping.

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[Hasini Wijayananda]

Dear Vikram,

Thank you so much for the suggestions and quick responses.