Hi, I am new in Galaxy. I want to ask related to get the .contree file and .treefile with bootstrapping value or confidence. I saw that in the .iqtree file but I want to generate it automatically from Galaxy. Thanks
Welcome, @Dhihram_Tenrisau
I’m not sure what you mean by automatically. Can you explain more? Maybe describe a bit about your starting data?
As a reference we have some tutorials that might help, or at least provide context.
- Evolution / Tutorial List (domain tutorials, all)
- Tutorials for IQ-TREE: Phylogenomic / evolutionary tree construction from multiple sequences (this is one example of the link you’ll find on the bottom of tool forms, if that tool is included in any)
- Tutorials for FASTTREE: build maximum-likelihood phylogenetic trees (another per-tool example)
Then there are tools not in tutorials – start in the Multiple Alignments tool group, or Evolution. Example: MSABOOT Output PHYLIP file with bootstrapped multiple sequence alignment data that can be used as input to a tool like Quicktree.
Maybe try to find a publication to follow that does what you want to do. You’ll probably find those tools or analogous open source tools in Galaxy. If you have a tool that does something and you can’t find that we have it yet, you can ask about it here.
Let’s start there, thanks!