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MCMC: does it show the probability on the branches? (Read 1868 times)
Sep 10th, 2019 at 9:51pm

morecoffee   Offline
YaBB Newbies

Posts: 4
Hello there,
I just did a first mcmc with UGENE, and I have some very low numbers on the branches, like 0, 0.001... is that the probability or the sd?
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Reply #1 - Sep 12th, 2019 at 2:18pm

Olga Golosova   Offline
YaBB Administrator

Posts: 338
We display "length_median" information, produced by MrBayes MCMC tool with the "Savebrlength" option enabled.

For details, see the original command-line tool documentation: http://mrbayes.sourceforge.net/Help/mcmc.html.

And see the attached files:
* tmp.nex.con.tre - output of the MCMC tool (note that the sequences are renamed).
* COI.nwk - the result Newick file, produced from this data

tmp_nex_con.tre (7 KB | 209 )
COI.nwk (0 KB | 209 )
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