map gene gain loss on species tree

Question

[Anand Rao]

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.

[moranr]

Did You ever find a solution to this ?

[Anand Rao]

http://www.cs.cmu.edu/~durand/Notung/

[Ric]

Could you provide more information on how you ran Notung?

Answer 1

[xmuraji]

you can try BadiRate.

[gnmcsbnfrmtcsclb]

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

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