I have a DNA alignment (representing genera), and a constraint tree (higher taxonomic level) and I want to use both data to generate a phylogeny.
The tree is based on a recent taxonomic classification that draws in morphological and phylogenetic data and is likely to be a much better representation of the taxonomy than my DNA sequences (which includes a lot of missing loci per genus) could ever provide.
There is quite a lot of taxa (~800) and so manually constraining different relationships is difficult (as can be achieved in BEAST and MrBayes).
What programs have other people used to combine DNA alignments with constraint trees to make a phylogeny?
I have used BEAST. However, if you think that your tree is a better representation that the phylogeny that you are trying to infer using DNA sequences, maybe you should use only that tree.
In my experience, using Beauti to manually constraint some clades can involve some time, but not too much. Of course, I had a tree with 300 taxa, not 800!!!
Other problem that can arise using constraints is when your constraints conflict with information from DNA sequences. So, my recommendation is to use the less number of constraints you can. Only those to help the algorithm to find those trees supported by several evidences beside DNA sequences you are using.
Good luck!
It is fairly straightforward to do this in Mesquite. Most helpful is that the matrix is directly linked to the topology, so you can simultaneously compare treescores as you manipulate the topology.
This can be easily done if running a RAxML phylogeny, especially if this is done on the CIPRES web portal. You need to create a constraint file. I usually do this in a good text editor such as TextWrangler (Mac) or Notepad++ (PC). Upload this file when setting your parameters. Here is an example of what your constraint file should look like:
((Taxa1, Taxa2),(Taxa3, Taxa4, Taxa5, Taxa6, Taxa7, Taxa8, Taxa9, Taxa10));
This would result in a tree were Taxa 1 and 2 are always sister, but the relationships of taxa 3-10 would be inferred by the analysis.
I also believe the above mentioned ML strategy is a good option (with RAxML). If you want to try a Bayesian approach as well, you can probably just run Beast or MrBayes for a fair number of generations, and extract the trees that produced the desired topology. Here's an example on how it was done using PAUP: http://www.sciencedirect.com/science/article/pii/S1055790314002267
I never actually tried, but I think you could just use Tree Annotator (distributed with Beast) to extract the trees from Beast or MrBayes runs (my guess is that it will be easier and faster than PAUP).
Good luck!
Hi, You can constraint a tree topology in mrbayes, using "constraint" and " prset topologypr " command
good luck
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