Question: map gene gain loss on species tree
0
gravatar for Anand Rao
5.0 years ago by
Anand Rao320
United States
Anand Rao320 wrote:

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.

 

ADD COMMENTlink modified 6 months ago by xmuraji0 • written 5.0 years ago by Anand Rao320

Did You ever find a solution to this ?

ADD REPLYlink written 4.1 years ago by moranr270

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

ADD REPLYlink written 4.1 years ago by Anand Rao320
0
gravatar for xmuraji
6 months ago by
xmuraji0
xmuraji0 wrote:

you can try BadiRate.

ADD COMMENTlink written 6 months ago by xmuraji0

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

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

ADD REPLYlink written 6 months ago by gnmcsbnfrmtcsclb30
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