Question: (Closed) RNA seq based phylogeny
gravatar for majeedaasim
2.5 years ago by
United States
majeedaasim40 wrote:

Through an RNA seq approach, I have identified 356 single copy orthologous groups across 9 species for their phylogenetic analysis. I now want construct species based phylogenetic tree.

What shall I do? Shall I merge all the genes of a species into a single super gene and do this for all species and then proceed for tree construction or not? How feasible and good it is.

If I simply use the individual genes of each species, I get a gene tree and not species tree.


rna seq phylogeny • 1.1k views
ADD COMMENTlink modified 2.5 years ago by h.mon30k • written 2.5 years ago by majeedaasim40

Hello majeedaasim!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


ADD REPLYlink written 2.5 years ago by genomax87k
gravatar for h.mon
2.5 years ago by
h.mon30k wrote:

You should concatenate all genes, but keep the information for each gene partition, because:

1) you may want to apply a model selection test on each gene and then estimate the phylogeny applying the selected model for each partition

2) you may want to test the stability of your final phylogeny in relation to gene sampling using a jackknife procedure.

Read some phylogenomics papers, then follow closely the methods from one or some of them. This one is a good start.

ADD COMMENTlink written 2.5 years ago by h.mon30k
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