need help with interpreting CAFE5 output

[Rosa Celia Poquita-Du]

Hello,

I am new to using Cafe5 and will need your help interpreting the output - "model_change.tab". In the documentation it says it is the difference between it and its parent clade in the reconstruction that was performed. 

Apologies if this sounds naive but what exactly is the parent clade? and do the signs '+ and -' before the count data means, expansion and contraction, respectively?

Also, I noticed that there are dummy taxa (shown as numbers) in the output files. I am only working on 7 species (one of it is an outgroup but a closely-related species) but there are additional columns for the dummy taxa with corresponding data for each gene family. I am wondering if the dummy taxa are only there to help with the modelling? Is there a minimum requirement of the number of species to run cafe5?

Hope to hear from you soon. Thank you for your help!

Cheers,

Ross 

[Hahn, Matthew]

Hi,

The numbering refers to nodes in the tree, including internal nodes. Such internal nodes represent “parents”, so that we can assign gains and losses to all branches of the tree (you are correct that + and - mean expansion and contraction, respectively). So by using the node numbers we can infer changes across the tree—no minimum number of taxa needed.

Matt

--
You received this message because you are subscribed to the Google Groups "hahnlab-cafe" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hahnlabcafe...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/hahnlabcafe/b2e2b8f1-1bf1-4723-b162-64308f27b391n%40googlegroups.com.

[Rosa Celia Poquita-Du]

Hi Matt,

I see, thank you very much for the clarification. Helps a lot!

Cheers,

Ross 

[Hahn, Matthew]

Hi Ross,

I guess I’m not sure what you’re asking for. CAFE does give a branch by branch accounting of all gains and losses, but no single number. You could sum together all gains and losses if you are looking for some sort of global tally.

cheers,

Matt

On Apr 2, 2024, at 8:33 AM, Rosa Celia Poquita-Du <poqui...@gmail.com> wrote:

Dear Matt, 

Hope it's okay continuing onto this email thread. I am trying to find a summary file generated from the cafe5 run I did previously but I couldn't find any. I wanted to find out the overall dynamic of gene family evolution (expansion or contraction) across the phylogeny of my study system. It appears that the global pattern is expansion but I wanted to find if cafe5 produces an output summary to support this, and whether the pattern has associated significant value. 

Thank you,

Ross 

To view this discussion on the web visit https://groups.google.com/d/msgid/hahnlabcafe/71944a3d-b33a-453d-acc4-cb2fa34d9f7an%40googlegroups.com.