Joao MF Alves

Understanding the *.samples file

1

Hi, I'm running SCITE using the -p option but I'm having difficulties understanding the actual output. So, the first line of the *.samples file looks like this: `-13.4636 41 0.000936101...

How to set more permissive parameters?

3

Hi, I’m currently running SCIPhI on some simulated sets but i’m getting some peculiar patterns and I’m not sure whether this is a bug of the tool or a misspecification...

Dear Victoria, Is there a simple way to extract the genotypes of the clones inferred by Lichee? While the output (*trees.txt) contains which mutations occur at which clone (and the...