Question

map gene gain loss on species tree

0

Entering edit mode

9.2 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 • 5.1k views

ADD COMMENT • link updated 2.1 years ago by Ric ▴ 440 • written 9.2 years ago by Anand Rao ▴ 640

0

Entering edit mode

Did You ever find a solution to this ?

ADD REPLY • link 8.3 years ago by moranr ▴ 290

0

Entering edit mode

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

ADD REPLY • link 8.3 years ago by Anand Rao ▴ 640

0

Entering edit mode

Could you provide more information on how you ran Notung?

ADD REPLY • link 2.1 years ago by Ric ▴ 440

score 0 · Answer 1 · 2020-03-20

0

Entering edit mode

4.7 years ago

xmuraji • 0

you can try BadiRate.

ADD COMMENT • link 4.7 years ago by xmuraji • 0

0

Entering edit mode

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

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

ADD REPLY • link 4.7 years ago by gnmcsbnfrmtcsclb ▴ 70