I constructed a ML tree using Mega6 and Bayesian tree using Mrbayes with same sequences but get different tree. What may be the possible reasons for this?
First - check if you can graphically rearrange the tree. It is possible without loosing information about support of branches.
Second - did you uuse the same substitution model and the same rate categories? It is important. Please, check it.
It is not surprizing at all. There can be several reason behind. As Agnieszka pointed out, you should double check the substitution parameters you used. For examle not all models are supported e.g in MrBayes which you can have in MEGA ML. Also there can be only orientational differences in the tree you got. If it so rearranging the tree you can have the very same topologies. And third, you can have different topologies because the phylogenetic signal of your gene(s) used is ot strong enought. In this case the weakly supported clades can appear differently using different methods.
As mentioned prior, please provide more detail on the differences between the topologies using Baysian and ML methods. To add to the above suggested reasons behind topological differences: MrBayes draws poorly supported nodes as polytomies while ML (in MEGA) will draw splits even with poor bootstrap support. Furthermore, I suggest you use Figtree or Mesquite to explore orientational differences.
Yes, FigTree (http://tree.bio.ed.ac.uk/software/figtree/) is really brilliant for manipulating trees.
- Badges
- Science method
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics
- Phylogenetic Analysis