Comments (8)
Hi Andrea,
You can label your tree with LabelTree.bf from this directory. Just clone the hyphy-analyses directory. To choose your test species you can list them in a text file as shown in the example hyphy-analyses/LabelTrees/data/data/list.txt. Then your command will look something like this:
hyphy ~/hyphy-analyses/LabelTrees/label-tree.bf --tree unlabeled.nwk --list list.txt --label "Test" --output labeled-parsimony.nwk --internal-nodes "Parsimony"
Then when you run FEL your branch name should match the label you chose (in this case Test)
hyphy fel --alignment nt.fasta --tree labeled-parsimony.nwk --branches "Test" --output nt.json
Let me know if you have any other questions.
Best,
Avery
from hyphy.
Dear @andrearam28,
you need label the branches in the tree.
from hyphy.
Hi @liamxg,
Thank you for your response.
I believe I do have all tips and nodes labelled, I can see them in the tree and when I open the tree in a program like Figtree.
I have tried other options and I am able to run contrast-fel with --branch-set "Random set of branches" for example. In the log I am able to see that internal nodes where randomly picked for this analysis, also. However, I am encountering issues regarding how to pick the specific branches I would like to use as test. This is where I get the error message that even one tip label "is not a valid choice passed to 'Choose sets of branches to compare."
Is there a specific format for this? I haven't been able to found it online and contrast-fel --help doesn't specify it either. Maybe something like a .txt file with all the branch names?
Thanks!
Andrea
from hyphy.
Dear @andrearam28,
you can do this in http://phylotree.hyphy.org/#.
from hyphy.
Hi @liamxg,
Thank you again for your response!
Is there a faster way to do this? If I need to run this test on 1,000 different sets of >300 sequences and pick 70-100 branches, I’m sure you can agree that this might not be the most efficient approach. I have the names of the branches I want to use as test. A faster/more efficient way would be extremely helpful!
Thanks again,
Andrea
from hyphy.
Dear @agselberg,
Thanks for your help.
BTW, how to only label the internal nodes not the tips?
from hyphy.
Liam,
You can use label-mrca.bf to label the most recent common ancestors of a given pair of taxa. See the readme with an example here.
Alternatively you can use LabelTree.bf to label the branches you don't want (in this case the tips of the tree) and use "Unlabeled branches" in your command. For example with BUSTED:
hyphy BUSTED --alignment positive-test.fasta --tree positive-test.nwk --branches "Unlabeled branches" --output practice.json
Best,
Avery
from hyphy.
Dear @agselberg,
Thanks again!
do you mean using the following command:
hyphy label-tree.bf --tree data/unlabeled.nwk --list data/list.txt --output only.nwk --internal-nodes None
and then using:
hyphy BUSTED --alignment positive-test.fasta --tree positive-test.nwk --branches "Unlabeled branches" --output practice.json
If so, this will test with BUSTED for all of the internal branches, right? But I want to label some clusters of internal branches as Alpha
, some internal branches as Delta
and the other internal branches as background
?
If I want to label like below, what should I do?
BTW, If I want to label only the internal branches of each Alpha
, Delta
and background
, what should I do, thanks.
![image](https://private-user-images.githubusercontent.com/46078579/360185631-4e46db8b-04ba-4995-acf8-72c42a56877f.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.qCxwyN0Qu5DiUs47UZEi00SokdZEr790IHln8Qdf0No)
from hyphy.
Related Issues (20)
- error HOT 7
- Analysis ends but does not progress to report generation HOT 5
- Failed to dereference error with FitMG94 and the local option HOT 2
- test for detecting compartmentalization in dataMonkey HOT 2
- DataMonkey not recognizing forground branches HOT 2
- MEME interpretation - 0 branches? HOT 4
- Different aBSREL results for same inputs HOT 11
- How to process the results files from OrthoFinder into input files for HyPhy ABSREL? HOT 9
- How to choose background branches? HOT 2
- Does excluding species with paralogous sequences violate aBSREL and/or RELAX assumptions of single-copy orthology? HOT 6
- Interpretation of RELAX across many genes HOT 2
- FADE: substitution model selection
- Multi-ORF Analysis Questions
- Barely any parallelism (max 110% CPU) running `hyphy gard` on macOS arm64 HOT 1
- GARD crashes when run on 27 SARS-CoV-2 sequences HOT 4
- Error when install hyphy using `conda install -c bioconda hyphy`?
- MEME HyPhy killed by signal 15
- The dN/dS ratio shows a significant difference between the foreground and background sets. Why is the result still that selection is not associated with the phenotype/trait? HOT 1
- Question about evidence of saturation in BUSTED / MEME output
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from hyphy.