Question: PAML CodeMl Dn/Ds help
0
gravatar for mti193
3.0 years ago by
mti1930
mti1930 wrote:

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.

codeml paml • 1.6k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by mti1930
0
gravatar for mti193
3.0 years ago by
mti1930
mti1930 wrote:

An update, I pasted the tree link which was a little bit further down under the category 'w ratios as labels for TreeView:' and basically got a phylogenetic tree where species one has a value of .148, but the rest of the 5 lineages all have a value of .3112

ADD COMMENTlink written 3.0 years ago by mti1930
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