Question

User-defined tree in MrBayes

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6.5 years ago

victoria_aleks ▴ 60

Dear all, I have a primitive question, I am afraid. I want to run MrBayes on amino acid sequences with the predefined tree, as random trees run does not reach conversion. Nevertheless, I can not find the command on how to do it. All the manuals and tutorials I have found say "User-defined trees can be read into MrBayes by executing a Nexus file with a ”trees” block" . That is followed by 'startvals' and 'npert'. I understand how to set the parameters for using the tree, but how to introduce the tree to Mr Bayes?

shortly: HOW can I READ IN the existing tree in MrBayes?

*'usertree' command resulted in the error message: "Usertree command deprecated. Define the tree in a treeblock and use 'Startvals' instead. Error in command "Usertree".

Thank you!

MrBayes Phylogeny Bayesian • 3.3k views

ADD COMMENT • link updated 6.5 years ago by h.mon 35k • written 6.5 years ago by victoria_aleks ▴ 60

score 2 · Accepted Answer · 2018-04-26

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6.5 years ago

h.mon 35k

See What do I do when it is difficult to get convergence from MrBayes FAQ:

begin trees;
  tree funkytree = ((runer:19.19959,newborn:6.80041):0.84600,((deacon:11.99700, neomorph:12.00300):7.52973,((protomorph:100.85930,facehugger:47.14069):20.59201, chestbuster:18.87953):2.09460):3.87382,praetorian:25.46154);
end trees;
begin mrbayes;
   startvals tau = funkytree V = funkytree;
end;

edit1: corrected extra semi-colon on tree.

edir2: as per victoria_aleks comment, I edited the tree block such as 'startvals tau = mytree' is in one line.

ADD COMMENT • link 6.5 years ago by h.mon 35k

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thank you! but then it says: "Could not find taxon 'Prot_ID' in list of taxa". what would that mean?

also, when I type: ... startvals tau = mytree -- it doesnt find the command 'tau', neither 'topology'

when I type: ... startvals tau = mytree --it doesnt know what is 'mytree' :(

ADD REPLY • link 6.5 years ago by victoria_aleks ▴ 60

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Probably formatting issues - for example, I just noticed my tree above has an extra semi-colon: praetorian:25.46154); ;. Also, it seems Prot_ID is found either at the tree and / or at the data blocks, but not at the taxa block.

Start with a small file - use the wikipedia toy example and build from that. Once you get the formatting right, then edit your real-world data set and try it.

ADD REPLY • link 6.5 years ago by h.mon 35k

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thanks, good idea. I spent already quite some time on all these small things...:) if i may ask: do you use MB often? My dataset is quite big (180 protein seq., ~100000 amino acids), and I have read that Mr Bayes is not good for big datasets...

ADD REPLY • link 6.5 years ago by victoria_aleks ▴ 60

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It has been a long time since I've used MrBayes, but indeed seems like a big data set, and should take a long time to run. Probably ExaBayes is a better option for this data set.

ADD REPLY • link 6.5 years ago by h.mon 35k

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it finally worked when I wrote 'startvals tau = mytree' in one line :) thank you again!

ADD REPLY • link 6.5 years ago by victoria_aleks ▴ 60

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Glad it worked. Please don't forget to follow up on your threads: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work. Upvote|Bookmark|Accept

Please do the same for your previous posts as well.

ADD REPLY • link 6.5 years ago by h.mon 35k