This web site is not a blog, even though it's a collection of random pieces of text on different subjects. However, I prefer more structure to the pages than the continuous flow common to the blog.
Screening orthologous genes for signs of selection can shed light on whether the genes are involved in adaption. It is important to design the experiment to include relevant contrasts for the question to be adressed. This python script uses MACSE to align the coding regions of transcripts/CDS-regions. Codeml from the PAML package of Ziheng Yang is then run on with the alignment. Finally, estimated parameters obtained with codeml can be exported. Typically, the log-likelihood of two different models can be obtained and used for the likelihood ratio test of goodness of fit.
The code can be found on GitHub.
Copyright © 2024 Mikael Durling. Published June 20, 2024.