search

dekoning-lab / slim-tree

4 stars 1 forks source link

Calculate dN and dS by counting fixations #64

Closed ebrintn closed 3 months ago

ebrintn commented 1 year ago

Use fixation counting commands to calculate dN and dS

ebrintn commented 1 year ago

Should be working now - @afarineshp can you check to see if you are getting the error you were getting before?

ebrintn commented 1 year ago

Fixed all bugs - see iss #37. Closing.

ebrintn commented 1 year ago

Talked in meeting about needing to add denominators from stationary distributions.

These values are really weird when implemented. I think we need to meet and talk more.

ebrintn commented 1 year ago

Not all codon distributions will be the same. Change to have users specify codon stationary distributions instead.

ebrintn commented 1 year ago

Updated with most recent push to include mutation matrices!

ebrintn commented 7 months ago

Counted each value of dN/dS and output the specific substitutions. Users can now see the denominators. I also fixed a bug in the way that fixations are determined. This may change the way that we were seeing substitutions before.

ebrintn commented 7 months ago

I definately think that it needs to be multiplied not divided by the selection coefficient we calculated