TreeMix software: Population history with migration

[Jonathan Pritchard]

In case you are interested, Joe Pickrell and I have just released a
companion program to Structure called TreeMix. TreeMix uses large
SNP data sets to estimate the relationships among populations
including both population splits and admixture events.

We think that the new method provides a better representation of
population histories than do standard tree-building methods when they
are applied to populations from the same species.

To get a better idea of what the program does, you can download a
preprint of the paper from here: http://precedings.nature.com/documents/6956/version/1

and you can get the software from here: http://code.google.com/p/treemix/

best wishes
Jonathan Pritchard

[Sampson, Jane]

Thanks!

Best,

Jane Sampson

best wishes
Jonathan Pritchard

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[Jonathan Pritchard]

TreeMix with microsatellites:   

Joe Pickrell has now released an updated version of TreeMix that allows the use of microsat data.  We think this is a useful tool for learning about the historical relationships among populations including migration events.   I should note that our main testing involved a rather large data set with several hundred microsats.  However, I expect that TreeMix will produce sensible results in smaller data sets, especially if the populations are more diverged than the populations that we looked at (a large number of human populations from Africa, many of which are very closely related).

Jonathan

[Jonathan Pritchard]

Sorry, I forgot to include the link:  https://code.google.com/p/treemix/

[Vu Thanh Nga]

Dear Jonathan Pritchard,

I'm using Treemix to estimate the relationships among 16 shrimp populations using SNPs. However, I don't know how to estimate the percentage of variance explained by each model.

Could you please guide me on how to estimate the percentage of variance explained by each model to find an optimal migration event?

Thanks for your help, I greatly appreciate it

Wish you all the best

Best regards

Nga

Vào 03:05:23 UTC+10 Thứ Ba, ngày 06 tháng 3 năm 2012, Jonathan Pritchard đã viết:

[Suany Quesada]

Dear Vu Thanh Nga

I just start to use Treemix.. But after loading the "plotting_funcs.R"  source, use the "get_f" function and you will get the values for each of your runs.

Have a nice day!

[Vu Thanh Nga]

Daer Suaby Quesada,

Thank you so much for your suggestion.

I have run the "get_f" function but it didn't work. The errors are:

- Error: unexpected string constant in "get_f = function(......

-  Error in order(names(d)) : argument 1 is not a vector

-  Error in order(names(d2)) : argument 1 is not a vector

I think the issue here is the (stem): get_f = function(stem){

d = paste(stem, ".cov.gz", sep = "")

........................

As I understand: The (stem) is the path to a directory containing stem.cov.gz and stem.modelcov.gz files produced by Treemix. Is it right?

If not, what should I write in The (stem)?

Many thanks

Kind regards

Nga

Vào Th 5, 23 thg 1, 2020 vào lúc 05:11 Suany Quesada <suan...@gmail.com> đã viết:

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[Suany Quesada]

Dear Vu Than Nga,

I would try using the path to a directory of stem, but I'm not sure if that is the solution ... sorry I am just starting to use treemix, but good luck!

Kind regards!

Suany

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