Hi all,
I performed ancestral state reconstruction (ASR) for immune proteins that showed positive selection. I am interested in assessing the amino acid changes at the internal branches where the bifurcation/duplication happened before speciation. I need some help understanding the result file for the ASR analysis. Please clarify my doubts. Here are my queries:
1. In the rst.txt file, it was mentioned that branches 265-526 are ancestral; however, according to the results (below), branch 266 is defined by species YBM_7. Am I inferring this correctly?
2. what does "266..398" represent? Does it signify the total number of internal/terminal branches present after branch 266?
These are the following branches that I am interested in:
"Branch 265: 266..398 (n=12.0 s= 3.0)
4 GGA (G 0.988) -> GGG (G) 1.000
5 ATT (I 0.999) -> ATC (I) 0.985
9 GCC (A 0.621) -> TCC (S) 0.975
14 AGA (R 0.552) -> GAA (E) 0.555
15 TTC (F 1.000) -> GTC (V) 0.418
Branch 266: 398..263 (YBM_7) (n=32.0 s= 8.0)
6 AAT (N 0.999) -> AAC (N)
7 ACC (T 0.894) -> ATC (I)
8 CCA (P 0.996) -> --- (-)
15 GTC (V 0.418) -> ACC (T)
16 AAG (K 0.449) -> CGG (R)
21 CCC (P 0.973) -> TCC (S)
For the sake of better understanding,
- Branch 265 is the root branch, and
- branch 266 is an internal branch
It would be really helpful if someone could help me understand the ancestral state reconstruction analysis result.
Thank you.
Regards
Nupur Nagar