Feature request phylogenetic analysis subworkflow

NBChub / bgcflow

Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)

https://github.com/NBChub/bgcflow/wiki

MIT License

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Feature request phylogenetic analysis subworkflow #261

Open OmkarSaMo opened 1 year ago

OmkarSaMo commented 1 year ago

I think it would be valuable to create a phylogenetic tree sub workflow.

autoMLST-based tree
GTDB tree using de_novo_wf
Roary core genome alignment tree

Perhaps we can add a compare_phylo rule to compare if different trees are in agreement with each other.

We can consider other options too.

@drboothtj let us know your thoughts on this sub-workflow that can do different relevant phylogenetic analysis.

drboothtj commented 1 year ago

This is definitely doable!

We can add getphylo and I have already written scripts for comparing trees and alignments. With a little tweaking I could formalise these scripts to produce a nice report (the current output is just text lines).

We could also add IQ-TREE for hardcore phylogenetics runs. I'm not experienced writing workflows but I'd be happy to work together to get these added!

matinnuhamunada commented 9 months ago

This is now implemented in the PR for v0.7.9 as a BGC subworkflow