-
Apologies for asking what is a very basic question about using TreeMix and OrientAGraph but I am hoping you can give me some advice. I am analyzing a set of 80 thousand SNPS that have already been fil…
-
Hi Simon,
I was trying to use phyml_sliding_windows.py, and use its result as the input of TWISS. But I found there were some issues on some occasions.
After using Beagle and VCF_processing/parseVCF…
-
Hi,
Firstly thank you so much for making these scripts - they look exactly what I was after.
I ran the following command:
```
bash ./Step1_TreeMix.sh ./file.treemix.frq.gz 64 100 Portugal 100 …
-
sometimes treemix has issues when loading a consensus tree. It's not clear where the problem is, maybe could be enough calculate the consensus trees with dendropy and find a way to visualize this tree…
-
I follwed the treemix commands, and it worked well.
However, I found an error in the last part of the treemix code
*this is my test.treemix.in.gz
Matsu Nemuro USA WGS
10,0 10,0 11,1 12,0
0,12…
-
Hey Andrew,
I'm plotting a treemix plot with popcorn (it's so great!) and I want to change the width of the lines -- both the lines making up the tree (to something like linewidth = 1) and the migrat…
-
I have run gimble v1.01 and v1.02(maybe). I think the functions of preprocess step is not complete.
Could you provide a shell script for preprocess ? It will be easy to seperate each step for work.…
-
Hi,
I'm using a single pulse admixture model to estimate the admixture time from one species to the admixed species. I got only one sample per species. When I was running Ancestry_HMM using the follo…
-
Hi!
I am trying to run the software in linux using the code below just for trial. I am sure that phylip exe works fine.
_sh ./Step1_TreeMix.sh populations.treemix.gz 1 3 noRoot 3 /home/yeserin/…
-
Hi there!
I have problems in installing/running the program in linux. I just unzipped scripts, and ran bash files with an input file that I got from stacks.
Below is the script that fails follo…