Question: Programs to View MrBayes Consensus Trees
0
gravatar for pld
5.0 years ago by
pld4.8k
United States
pld4.8k wrote:

I've tried several web tools that draw trees in newick formatting, but outside of the nexus formatting, the MrBayes *.con.tre file seems to contain a ton of extra stuff. Any suggestions for programs that can draw the trees directly from this file, or what needs to be changed in the file to make it possible to draw with programs that take only newick format?

 

For example: I've tried FigTree, but any attempt to open a .con.tre file results in an error stating "Missing closing ")" in tree"
 

Can someone post a working con.tre file for me to compare my file against? I'm fine with manually fixing the files if I only knew what to look for.

mrbayes • 5.0k views
ADD COMMENTlink modified 3.2 years ago by pawan.mishra180 • written 5.0 years ago by pld4.8k

i do have same problem can you tell me hoe to fix this as I am unable to understand why it is shoe missing ")" in tree

ADD REPLYlink written 3.2 years ago by pawan.mishra180
1
gravatar for Zev.Kronenberg
5.0 years ago by
United States
Zev.Kronenberg11k wrote:

I have successfully used FigTree with MrBayes consensus trees.  Here is the command block I used and then directly imported into FigTree.

 

#NEXUS
begin mrbayes;
    execute nels.nexus;
    mcmcp filename = tree1;
    Prset Aamodelpr = fixed(rtrev);
    mcmc nchains = 4 ngen = 500000;
    sumt relburnin = yes burninfrac = 0.25;
    sump relburnin = yes burninfrac = 0.25;
    sump;
    sumt;
end;

 

ADD COMMENTlink written 5.0 years ago by Zev.Kronenberg11k

That is more or less what I ran:

execute xxxx.nexus;
lset nst=6;
lset rates=invgamma;
mcmcp ngen=10000000;
mcmcp samplefreq=10;
mcmcp nruns=3;
mcmcp nchains=40;
mcmcp relburnin=yes;
mcmcp burninfrac=0.20;
mcmcp mcmcdiagn=yes;
mcmcp diagnfreq=500;
mcmc;
sumt;
sump;

Which file are you loading into FigTree?

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by pld4.8k

*.con.tre 

ADD REPLYlink written 5.0 years ago by Zev.Kronenberg11k

This is frusterating, which version of MrBayes are you using, maybe there is an issue there.

ADD REPLYlink written 5.0 years ago by pld4.8k

Yes, it really is.  fig tree-1.0.4 and MrBayes-3.2.2.  

ADD REPLYlink written 5.0 years ago by Zev.Kronenberg11k
1

I managed to fix it, there were newline characters in the tree string.

ADD REPLYlink written 5.0 years ago by pld4.8k
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