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.
thanks
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written
by
majeedaasim •
1 answer
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.
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