Map gene presence/absence (i.e. gain, loss, duplication) on phylogenetic tree

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4.4 years ago

djamalova.d ▴ 10

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 ( http://www.frontiersin.org/files/Articles/89536/fpls-05-00299-HTML/image_m/fpls-05-00299-g003.jpg ).

phylogeny pangenome • 1.1k views

ADD COMMENT • link updated 4.4 years ago by Michael 54k • written 4.4 years ago by djamalova.d ▴ 10

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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 REPLY • link 4.4 years ago by Michael 54k

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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 REPLY • link 4.4 years ago by djamalova.d ▴ 10

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