Question: Map gene presence/absence (i.e. gain, loss, duplication) on phylogenetic tree
gravatar for djamalova.d
6 weeks ago by
djamalova.d10 wrote:

I got PGL (propensity for gene loss) output as counted gene gain/loss. I couldn't extract it as a phylogenetic tree. Is there any software where I can manually write all these numbers on phylogenetic tree or can I perform it via biopython?

Here is a link for a picture showing which result I would like to get ( ).

pangenome phylogeny • 109 views
ADD COMMENTlink modified 6 weeks ago by Michael Dondrup47k • written 6 weeks ago by djamalova.d10

Maybe you can do with the ETE library. I am guessing you have files in the format of "taxid propensity"? You need to generate or download a phylogenetic tree for your taxa that has the same nodeIDs for all interior AND leaf nodes as in your PGL file. Possibly, you could help us by posting an example file.

ADD REPLYlink written 6 weeks ago by Michael Dondrup47k

Thank you for your response. I have a species tree and output file from ProteinOrtho5. I converted it into binary (0,1) and loaded it into Count software. There I performed PGL analysis which gave me a number of gain/loss per node. When I tried to extract it I got the same proteinortho file.

ADD REPLYlink written 6 weeks ago by djamalova.d10
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