Question: looking for a tree viewer useful for .con.tre file outputted from MrBayes
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gravatar for ricfoz
16 months ago by
ricfoz30
National School of Antropology and History, Mexico city, Mexico
ricfoz30 wrote:

Hello community,

I have run a Marcov Chain Monte Carlo analysis usin MrBayes. It run succesfuly and outputted (besides a few other files) a consensus .con.tre file which i was able to print in a tree viewer called FigTree-v1.4.3; it was pretty useful, but i have some branches which are short, and overlap on each other since i can't zoom enough in order to view some of the clades.

Since i have this problem, i just wanted to ask the community for another tree viewer which anyone knows to be able to zoom in enough to see short branches. Any suggestion will be much appreciated.

Sincerely

Ricfoz.

treeviewer tree viewer mrbayes • 499 views
ADD COMMENTlink modified 16 months ago by Kevin Blighe48k • written 16 months ago by ricfoz30
0
gravatar for Kevin Blighe
16 months ago by
Kevin Blighe48k
Kevin Blighe48k wrote:

You should be able to use FigTree: http://tree.bio.ed.ac.uk/software/figtree/

Please see this previous posting: Programs to View MrBayes Consensus Trees

You may additionally find utility in looking at the methods of this published work, where they initially used MrBayes but then bootstrapped their tree outside of MrBayes, followed by the generation of a distance matrix from the bootstrapped results: A "green" phosphoribulokinase in complex algae with red plastids: evidence for a single secondary endosymbiosis leading to haptophytes, cryptophytes, heterokonts, and dinoflagellates..

They used MyBayes and then generated distance matrices (from which a tree can easily be plotted in R) using various programs/packages:

All phylogenetic treespresented are MrBayes consensus trees; in the corresponding treesthe posterior probabilities are displayed as percentages. Bayesianinference was performed with the program MrBayes version 3.0B4(Huelsenbeck and Ronquist 2001) using the WAG+F+I+G4model. Usually 200,000 generations were completed with treescollected each tenth generation; the number of generations neededuntil the likelihood values converged (burn-in) was typically lessthan 5%of the total. Maximum likelihood (ML) bootstrap values(100 replicates) were calculated with the program PHYML version2.4 using a WAG+F+I+G8 model (Guindon and Gascuel 2003).Furthermore, a distance-based approach (ML distances usingWAG+F+I+G8 model) was done using the program TREE-PUZZLE version 5. 2together with the unix shell script PUZ-ZLEBOOT (http://hades.biochem.dal.ca/Rogerlab/Software/soft-ware.html), the trees were obtained using the program BIONJ(Gascuel 1997), and the bootstrap consensus tree (1000 replicates)was subsequently generated by the CONSENSE option of thePHYLIP package (Felsenstein 2004)

Kevin

ADD COMMENTlink written 16 months ago by Kevin Blighe48k
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