Hello everyone,
I am a very new user of MrBayes 3.2. Please help with my doubt.
I have constructed a phylogenetic tree of 43 sequences using MEGA and MrBayes. I have attached both the files here. I am getting a correct tree pattern in MEGA_Neighour joining.nwk tree file as expected. But in MrBayes.con.tre tree, Rabbit_CXCL1 and Rabbit_CXCL2 are seperated from the entire tree, even though the nucleotide sequences of those two are not so different than rest of the sequences. I want a MrBayes tree with those two sequences incorporated. So, apart from .con.tre, can I use some other tree from MrBayes output file?
There are many trees in .t file. Can I choose any one among them? Or is there a particular criteria to select one?
Thank you in advance.
Regards,
Minal
Hi MianI,
You absolutely can NOT choose a tree from .t file. They are just mcmc sample of trees. You should only use the consensus tree summarized from those trees in .t file, that is the .nex.con file you attached here.
Actually, as far as the major clades concerned, the MrBayes tree is largely congruent with the NJ tree. The different you described seems due to your misunderstanding about phylogenetic tree. Have a second look at your trees as follows.
1. root two trees with the same nodes
2. swap and rotate subclades
Find some references to get some general idea about phyogenetic tree will help. Phylogenetic tree is not a graph.
best
As Chengmin Shi says, you must use the same out group to root the tree in order to be able to compare them, and when you do that, the trees are mostly congruent. the trees in the .t file are all the trees sampled, I guess you could use a maximum clade credibility tree, as is used be e.g. BEAST, but I would not recommend it. the consensus tree shows the relationships that are found in a majority of trees. and if you look at the posterior probabilities, you can see that many clades have low support, which means that you cant trust those relationships
As long as you do not want to do any fancy things like doing your own post analysis of the markov chain of hypotheses, only the consensus tree is of interest for you.
I do not understand what the problem is with the two sequences being separated from the rest of the tree. Each group of two sequences are separated from the rest of the tree. Your NJ tree is a cladogram without branch lengths. Therefore the amount of separation cannot be compared among the two trees.
Best Christoph
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