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Hi,
Can you give me an example of graph file that transformed from treemix results?
Thank you!
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Hi,
First of all thanks a lot for this package.
I run this command (Rstudio with R version 3.5.1; Ubuntu 16.04LTS) but there were problems:
genepop_treemix("input_genepopedit_4360.txt",where.pl…
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Thanks for all the help you have provided everyone here!
I generated the smc estimate input from vcf2smc with zero problems. When I throw this into estimate I get an error (see .err file attached).…
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First of all thank you for the great package!
I encountered a problem when using the recent versions of ipyrad and toytree together:
python version: 2.7.15,
ipyrad version: 0.7.28 (py27ha9968…
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Hi there,
I was very excited to try out the new script for converting a gl to a treemix file but it doesn't seem to have worked. It took a long time to process (20812 snps in the gl) and it created…
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Looks pretty straightforward. From the manual:
```
By default, TreeMix assumes biallelic sites. The input file is a gzipped file that consists of a header
with a space-delimited list of the names o…
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This was a popular option in pyrad that allows filtering your data such that there are at least N samples per population per locus. I figure we should implement this first, then we can add the populat…
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https://bitbucket.org/nygcresearch/treemix/downloads.
TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, …
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Applies to biipy v2.1.0:
```
ImportErrorTraceback (most recent call last)
/media/aliman/SD1/src/github/malariagen/ag1000g/notebooks/aliman/imports.ipynb in ()
19 from IPython.display import clea…
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It would be useful on many fronts to have a population assignments file passed in or set as a parameter. Output formats use this (migrate/treemix), D stats uses this, hierarchical clustering would use…