map gene gain loss on species tree
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8.8 years ago
Anand Rao ▴ 640

With what software tool can I reconcile the gene tree (obtained for orthologs using OrthoFinder) versus the species tree for ~ 30 plant species?

I was thinking of using NOTUNG, but realized it may not output the specific image I am looking to generate.

Which is: ready-made tree that has the gain and loss numbers of the orthologs mapped on to internal nodes and terminal leaf nodes of the species tree.

Something like what I find in these example images : , or .

Please note that I am currently not using an outgroup species, or outgroup sequences for gene tree.

gene-tree tree reconciliation species • 4.8k views
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Did You ever find a solution to this ?

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Could you provide more information on how you ran Notung?

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4.3 years ago
xmuraji • 0

you can try BadiRate.

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http://www.ub.edu/softevol/badirate/

I suppose this is the software that xmuraji is referring to?

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