bootstrapping and consensus tree by TREEMIX

[Chee Wei Yew]

Dear All,

I notice that different runs of bootstrapping (-bootstrap -K ) by TREEMIX, with the same settings will generate trees of different topology. As such, the main clades of the tree topology is always the same across the runs, but the smaller clades, which I made up of populations that might be admixed, are always different. I would like to obtain a consensus tree topology out of multiple independent runs (e.g. 100 trees).

My question:

How to obtain a consensus tree? is there commands for this in TREEMIX?

Thanks!

Regards,
Yew

[Jane]

Hi Yew, 

    Did you figure out how ? I am having the same issue. The solution I can think is to make a number bootstrap replicates (refer to the manual) and create consensus tree in some other program, like Phylip :http://evolution.genetics.washington.edu/phylip/doc/consense.html

   But I have no clue how to deal with the migration though. 

Jane

[Chee Wei Yew]

Hi Jane,

Unfortunately, I haven't figured it out yet. I just wonder how the author of the treemix paper did it. Have a look at their large treemix-tree, with all HGDP populations, I am sure there is a way to construct such a tree which is good for presentation and publication.

I tried to use the instruction given in the manual under the section 'Input a previously generated tree/graph (-g)'. It does not work also.

Yea, I use phylip to draw ML and NJ trees, but it doesn't have the migration direction, which is essentially the soul of TREEMIX.

I am currently busy with my writing. When I am free, I will try to ask the authors directly. If I got good news, I will let you know.

Thank you.

Regards,

Chee Wei

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[Joseph Pickrell]

Hi all, 

For building consensus trees from different bootstrapped treemix runs, I used sumtrees in the dendropy package: http://pythonhosted.org/DendroPy/programs/sumtrees.html

I unfortunately don't have a way of visualizing bootstrapped graphs in a satisfying way. 

Best, 

Joe

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[Gislaine]

Hi Joe, 

Is so important make the consensus tree with bootstrap? Because In my case, even with NJ or UPGMA I didn't recovery good support for the branches, except to one group that is my outgroup, that I fixed as a root in treemix. So my question is if I can discuss the results without the bootstrap of the tree (considering the low support to ingroup from NJ and UPGMA), but considering the likelihood values from different runs of migration and considering the residual plot. Can I do it?

Thanks 

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[Nikki Phair]

Hello,

I see that this thread is not very recent but I thought I'd take a chance anyway. I have been playing around with the Treemix parameters, the manual is very basic, and I'm not sure what is best for my study... My biggest question right now is where do I find the bootstrap values? and to run for example 100 replicates, do I literally need to run "treemix -i infile.gz -o outstem1-100 -bootstrap -k 500 -m 10 -se" 100 times?

When I plot my trees the bootstrap values don't show up and there is no handy output labled 'bootstrap values'. Any advice?

Thanks in advance,

Nikki

[Adrián Casanova Chiclana]

Hi everyone,

Maybe one option could be this Rpackage : https://github.com/marcomilanesi/BITE

"BITE implements additional useful procedures, such as representative sampling and bootstrap for TreeMix, filling the gap in existing biodiversity data analysis tools."

I will try it.

[elizabet...@gmail.com]

Hello everyone,

Has anyone found a good solution or code to address this question (labeling a treemix tree with bootstrap support results)?  The documentation for the BITE package is incomplete, and the author of the program said that they have not finished the documentation yet.

Any guidance on this topic would be much appreciated.

Thanks!

Elizabeth

[Suany Quesada]

Hi everyone,

I ran the bash script "Treemix_bootstrap.sh"  from the BITE web page https://github.com/marcomilanesi/BITE/wiki/How-to-run-Treemix-analyses  but I got a error message  "export: Illegal option -f " ....

I followed the instructions and have tried to find how to fix the error but could not... Has anyone the solution???

My comand line was:

     sh ./BITE-master/BITE_1.2.0007/BITE/inst/scripts/treemix_scripts/Treemix_bootstrap.sh populations2.treemix.gz 3 6 500 NoOutgroup 10 ./ pru
      **** RUNNING TREEMIX ****
     ./BITE-master/BITE_1.2.0007/BITE/inst/scripts/treemix_scripts/Treemix_bootstrap.sh: 54: export: Illegal option -f

Thanks in advance,

Have a nice day!

[Vikram Chhatre]

The best people to help with this are the ones who wrote the bash script. I suggest opening a new issue on their Github page.

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[Suany Quesada]

I will do that! Thank you!!

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