stevenweaver
commented
1 month ago Dear @sophie-03,
For calculating dN/dS values for every branch in your phylogenetic tree, using aBSREL (Adaptive Branch-Site Random Effects Likelihood) in HyPhy is appropriate. aBSREL is designed to detect episodic diversifying selection at the level of individual branches and provides a distribution of dN/dS ratios for each branch.
If you navigate your browser to http://vision.hyphy.org/absrel, we can take a look at the phylogenetic tree plot.
Plot Explanation
1. Color Scale for ω (dN/dS) Values:
- The color scale at the top of the plot indicates the dN/dS (ω) values, with blue representing low ω values (purifying selection), grey representing neutral evolution, and red representing high ω values (positive selection).
- The scale ranges from 0.0001 to 1000, indicating the range of dN/dS values observed in the branches.
2. Branch Coloring:
- Branches are colored according to the proportion of sites fitting into different ω categories (purifying, neutral, and positive selection):
- Blue Branches: These branches have a high proportion of sites with low ω values (dN/dS < 1), suggesting purifying selection.
- Grey Branches: These branches have a high proportion of sites with ω values around 1, indicating neutral evolution.
- Red Branches: These branches have a high proportion of sites with ω values greater than 1, indicating positive selection.
- The mixed coloring on branches shows the proportion of sites under different selection pressures, with a gradient reflecting the relative proportions.
3. Branch Lengths:
- The horizontal length of each branch is proportional to the number of substitutions per site. Longer branches indicate a higher number of substitutions, which could be due to longer evolutionary time or higher mutation rates.
4. Tips of the Tree:
- The names at the tips of the tree (e.g., HLmyaMyo6, HLrhiFer5) represent the taxa or sequences included in the phylogenetic analysis.
Interpretation of the Plot
- Proportional Selection Representation: The branches are colored based on the proportion of sites under different selection categories. For example, a branch that is mostly blue with some red suggests that most sites are under purifying selection, but some sites are experiencing positive selection.
- Positive Selection: Branches with a large proportion of red indicate a high proportion of sites under positive selection.
- Purifying Selection: Branches with a large proportion of blue indicate a high proportion of sites under purifying selection.
- Neutral Evolution: Branches with a large proportion of grey indicate a high proportion of sites evolving neutrally.
Summary
- Blue branches: High proportion of sites under purifying selection (dN/dS < 1).
- Grey branches: High proportion of sites under neutral evolution (dN/dS ≈ 1).
- Red branches: High proportion of sites under positive selection (dN/dS > 1).
- Mixed colors: Proportional representation of sites under different selection pressures.
- Branch thickness: Associated p-value (The smaller the p-value, the thicker the branch).
If you would like to analyze the raw JSON output of aBSREL, documentation is found at https://hyphy.org/resources/json-fields.pdf.
If you would like a more complete introduction to HyPhy, please see the reference page on the site, https://hyphy.org/resources/.
Best, Steven
sophie-03
spond
Hi,
I would like to calculate dN/dS values for every branch branch in my phylogenetic tree. I have looked into the different hyphy commands and I am struggling to identify which would be best. I have tried absrel but I am unclear on the output. Am I correct in using the absrel function if I would like to to obtain an average dN/dS value for every branch of the tree? If so, is there any documentation that explains the output?
Thanks.