Specifying foreground and interpret results

[chenyangkang]

Hi it's me again :)

I wanna know if the tree ((A{Foreground}, B{Foreground}), C); is the same as ((A, B){Foreground}, C); for aBSREL model. That confused me a little bit.

Another thing is how to know the output like "Node22". How can I know which Node it is? Is there an ordered way that you annotate these nodes?

Thanks!

Yangkang

[spond]

Dear @chenyangkang,

1. Your first two examples are not the same

If you paste your trees into http://phylotree.hyphy.org you will see the effect

vs

2). Internal node names are generated in "post-order" traversal. You can see what they are in several ways.

You can use visualization tools like http://vision.hyphy.org/absrel?resultURL=https://data.hyphy.org/web/swap/nt_coding_spurceup.phy.ABSREL.json

You can look at JSON files to get annotated trees with internal nodes labeled

You can also just name the nodes in your Newick String, e.g. ((A, B)my_node{Foreground}, C)

3). aBSREL tests each branch separartely. By specifying "foreground" you simply ask it to only test a subset of branches (one at a time). PAML treats them all as a group. With PAML you want some form of a free-ratio model, or you need to specify a single branch as foreground. A more direct analog to what PAML is doing is HyPhy's BUSTED.

Best, Sergei

[chenyangkang]

@spond Thanks for such a quick reply! Deeply appreciated!

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