- I have several .tree files derived from the same BEAST file ran on different computers but I need to perform a consensus on those trees, is there a program for that?
Instead of constructing a consensus tree I would use LogCombinder (included in the beast package) to combine them the .tre files to a single file. If you do not have a specific reason to want a consensus tree.
I do not know the type of the output tree file in BEAST but you can try to use the consense program of the PHYLIP package. It can generate different consensus trees. http://evolution.genetics.washington.edu/phylip/doc/consense.html
Provided it is the same xml input file you created with Beauti that ran on the different computers (or even on the same computer as different runs), then you can use log-combiner which is found in the Beast package. The program will ask you if you want to combine log files or tree files and how many generations or trees to ignore (burnin) from each run/file. You select the tree files you want to combine, the burnin and the name of the output file and then the programme ignores the burnin trees and puts all remaining trees from all runs in the same huge tree file. You can then use that one with tree-annotator (again in the Beast package) and make your favourite consesus tree. This time use zero burnin - you've already done that for each run separately. Make sure that your separate runs have actually converge before doing all the above and you might also need to repeat it a couple of times with different burnin because it tends to run out of java memory when your combined-trees file is too large.
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