Hi, so I have been looking at previous posts and online examples and I feel like I am almost there in what I wanna do.
Basically i have 3 land mammals and 3 marine mammals. I hope to see a higher rate of Dn/Ds (positive selection) for the marine mammals due to selective pressure of the environment on them as opposed to the land mammals.
I ran the 'null' model, and received these results:
kappa (ts/tv) = 2.09083
omega (dN/dS) = 0.30468
Then (trying to use a branch model) and I'm not sure if i'm doing it right because I see an option for codeML after Nsites (2, positive selection) But I basically just changed nullmodel fro 0 to 2 and ran it and got the result
kappa (ts/tv) = 2.08985
w (dN/dS) for branches: 0.31127 0.14794 and a really complicated
branch t N S dN/dS dN dS NdN SdS
7..8 0.056 336.1 101.9 0.3113 0.0123 0.0394 4.1 4.0
8..9 0.129 336.1 101.9 0.3113 0.0283 0.0909 9.5 9.3
9..10 0.102 336.1 101.9 0.3113 0.0224 0.0718 7.5 7.3
10..1 0.031 336.1 101.9 0.1479 0.0045 0.0303 1.5 3.1
10..2 0.004 336.1 101.9 0.3113 0.0008 0.0027 0.3 0.3
9..3 0.041 336.1 101.9 0.3113 0.0089 0.0287 3.0 2.9
8..5 0.306 336.1 101.9 0.3113 0.0674 0.2166 22.7 22.1
7..4 0.206 336.1 101.9 0.3113 0.0454 0.1460 15.3 14.9
7..6 0.397 336.1 101.9 0.3113 0.0874 0.2807 29.4 28.6
What am i missing here? Thanks for anyone that helps.
