How to start with gappa

[NailouZhang]

Hi,
I'm lucky enough to get to know Gappa. It's a versatile tool for analyzing and visualizing phylogenetic data. I want to convert a taxonomy of tab files into tree files and visualize these trees with different abundances between the groups, do something as displayed in your acticle. But it's hard for me to start with Gappa. Could you show me a tutorial or examples for this?
Although I have read you article "Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data." and "Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade.", there are some concepts I have a hard time understanding. Could you give me some easy-to-read articles?

[lczech]

Dear @NailouZhang,

I'm lucky enough to get to know Gappa. It's a versatile tool for analyzing and visualizing phylogenetic data.

Thank you!

I want to convert a taxonomy of tab files into tree files and visualize these trees with different abundances between the groups, do something as displayed in your acticle. But it's hard for me to start with Gappa. Could you show me a tutorial or examples for this?

The taxonomy-tree command might help, if I'm understanding you correctly. But I don't know which plots you are referring to, so I cannot tell you which tools to use for the visualizations. The gappa wiki contains all commands - just have a look there. For your taxonomy, you might also be interested in Krona plots.

Although I have read you article "Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data." and "Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade.", there are some concepts I have a hard time understanding. Could you give me some easy-to-read articles?

Well, the review article is meant as an introduction to the topic. I suggest reading up on the literature that is mentioned there, in particular the other phylogenetic placement papers, and to start playing around with your data and the tools. Other than that, Google, ChatGPT, etc might also help you to answer further questions you have. Without further information on what those hard concepts are, I'm afraid I cannot help much here.

Hope that helps
Lucas

[lczech]

Hi @NailouZhang,

as you do not seem to have any follow up questions, I'll close the issue now. Feel free to re-open should you need further information.

Also, I wanted to mention that my PhD thesis actually might contain a more detailed introduction to some of the topics, and might help you: https://publikationen.bibliothek.kit.edu/1000105237

Cheers
Lucas