Format for selecting branches to test on FEL about hyphy

[agselberg]

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

[liamxg]

Dear @andrearam28,

you need label the branches in the tree.

[andrearam28]

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

[liamxg]

Dear @andrearam28,

you can do this in http://phylotree.hyphy.org/#.

[andrearam28]

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

[liamxg]

Dear @agselberg,

Thanks for your help.

BTW, how to only label the internal nodes not the tips?

[agselberg]

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

[liamxg]

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.