Web document 7.11. Sample output from a Bayesian phylogenetic analysis using MrBayes.
Logging screen output to file "log.out"
MrBayes > sumt
Summarizing trees in files "13globins.nex.run1.t" and "13globins.nex.run2.t"
DOS line termination
Examining first file ...
Found one tree block in file "13globins.nex.run1.t" with 5944 trees in last block
Expecting the same number of trees in the last tree block of all files
Tree reading status:
0 10 20 30 40 50 60 70 80 90 100
v-------v-------v-------v-------v-------v-------v-------v-------v-------v-------v
*********************************************************************************
Read a total of 11888 trees in 2 files (sampling 11888 of them)
(Each file contained 5944 trees of which 5944 were sampled)
File "13globins.nex.parts" already exists
Overwrite information in this file (yes/no): Overwriting file "13globins.nex.parts"
File "13globins.nex.con" already exists
Overwrite information in this file (yes/no): Overwriting file "13globins.nex.con"
File "13globins.nex.trprobs" already exists
Overwrite information in this file (yes/no): Overwriting file "13globins.nex.trprobs"
General explanation:
A taxon bibartition is specified by removing a branch, thereby dividing the
species into those to the left and those to the right of the branch. Here,
taxa to one side of the removed branch are denoted "." and those to the
other side are denoted "*". The output includes the bipartition number
(ID; sorted from highest to lowest probability), bipartition (e.g., ...**..),
number of times the bipartition was observed (#obs), the posterior probabil-
ity of the bipartition, and, if branch lengths were recorded on the trees in
the file, the average (Mean(v)) and variance (Var(v)) of the lengths. Each
"." or "*" in the bipartition represents a taxon that is to the left or
right of the removed branch. A list of the taxa in the bipartition is given
before the list of bipartitions. If you summarize several independent analy-
ses, convergence diagnostics are presented for both the posterior probabil-
ities of bipartitions (bipartition or split frequencies) and branch lengths
(if recorded on the trees in the files). In the former case, the diagnostic is
the standard deviation of the partition frequencies (Stdev(s)), in the second
case it is the potential scale reduction factor (PSRF) of Gelman and Rubin
(1992). Stdev(s) is expected to approach 0 and PSRF is expected to approach 1
as runs converge onto the posterior probability distribution. Note that these
values may be unreliable if the partition is not present in all runs (the
last column indicates the number of runs that sampled the partition if more
than one run is summarized). The PSRF is also sensitive to small sample
sizes and it should only be considered a rough guide to convergence since
some of the assumptions allowing one to interpret it as a true potential
scale reduction factor are violated in the phylogenetic context.
List of taxa in bipartitions:
1 -- mbkangaro
2 -- mbharbor_
3 -- mbgray_se
4 -- alphahors
5 -- alphakang
6 -- alphadog
7 -- betadog
8 -- betarabbi
9 -- betakanga
10 -- globinlam
11 -- globinsea
12 -- globinsoy
13 -- globinins
Summary statistics for taxon bipartitions:
ID -- Partition #obs Probab. Stdev(s) Mean(v) Var(v) PSRF Nruns
--------------------------------------------------------------------------------
1 -- ..*.......... 11888 1.000000 0.000000 0.043107 0.000418 1.000 2
2 -- ......*...... 11888 1.000000 0.000000 0.070789 0.000586 1.000 2
3 -- .........*... 11888 1.000000 0.000000 0.037674 0.000654 1.001 2
4 -- ..........*.. 11888 1.000000 0.000000 0.064191 0.000791 1.002 2
5 -- ...*......... 11888 1.000000 0.000000 0.088738 0.000754 1.000 2
6 -- .************ 11888 1.000000 0.000000 0.116869 0.001562 1.000 2
7 -- .*........... 11888 1.000000 0.000000 0.067826 0.000461 1.000 2
8 -- ...........*. 11888 1.000000 0.000000 0.852265 0.033478 1.001 2
9 -- ....*........ 11888 1.000000 0.000000 0.105215 0.001036 1.000 2
10 -- .....*....... 11888 1.000000 0.000000 0.126253 0.001089 1.000 2
11 -- ............* 11888 1.000000 0.000000 0.756330 0.026074 1.000 2
12 -- .......*..... 11888 1.000000 0.000000 0.083162 0.000663 1.000 2
13 -- ........*.... 11888 1.000000 0.000000 0.158580 0.001857 1.000 2
14 -- ...********** 11886 0.999832 0.000000 0.675390 0.023884 1.000 2
15 -- ...***....... 11885 0.999748 0.000119 0.328362 0.005318 1.000 2
16 -- .........**.. 11885 0.999748 0.000119 0.505679 0.014589 1.000 2
17 -- ......***.... 11879 0.999243 0.000119 0.295652 0.005753 1.001 2
18 -- ...*.*....... 10654 0.896198 0.006186 0.051493 0.000632 1.000 2
19 -- ...........** 10577 0.889721 0.005353 0.433231 0.016810 1.000 2
20 -- ......**..... 10281 0.864822 0.004402 0.061645 0.000833 1.000 2
21 -- ...******.... 10097 0.849344 0.009398 0.223350 0.007999 1.000 2
22 -- .........**** 6260 0.526581 0.002141 0.225533 0.009590 1.000 2
23 -- .**.......... 5840 0.491252 0.006186 0.049463 0.001080 1.000 2
24 -- ..*********** 5284 0.444482 0.005234 0.026841 0.000303 1.000 2
25 -- ...********.. 4253 0.357756 0.008208 0.224796 0.010708 1.002 2
26 -- ...*********. 1288 0.108345 0.005234 0.331364 0.013494 1.005 2
27 -- ...******..*. 1154 0.097073 0.008327 0.251456 0.008839 1.000 2
28 -- ...**........ 1147 0.096484 0.006781 0.037934 0.000569 1.002 2
29 -- ......*.*.... 1111 0.093456 0.002498 0.029859 0.000319 1.000 2
30 -- ...***...**** 830 0.069818 0.005948 0.122319 0.003635 1.013 2
31 -- .*.********** 762 0.064098 0.000952 0.015361 0.000199 1.000 2
--------------------------------------------------------------------------------
Clade credibility values:
/---------------------------------------------------------------- mbkangaro (1)
|
|---------------------------------------------------------------- mbharbor_ (2)
|
|---------------------------------------------------------------- mbgray_se (3)
|
| /------------- alphahors (4)
| /-----90-----+
| | \------------- alphadog (6)
+ /----100----+
| | \-------------------------- alphakang (5)
| |
| /-----85-----+ /------------- betadog (7)
| | | /-----86-----+
| | | | \------------- betarabbi (8)
| | \----100----+
| | \-------------------------- betakanga (9)
\-----100----+
| /------------- globinlam (10)
| /-----100----+
| | \------------- globinsea (11)
\-----------53-----------+
| /------------- globinsoy (12)
\-----89-----+
\------------- globinins (13)
Phylogram:
/--- mbkangaro (1)
|
|-- mbharbor_ (2)
|
|- mbgray_se (3)
|
| /--- alphahors (4)
| /+
| |\---- alphadog (6)
+ /---------+
| | \--- alphakang (5)
| |
| /-----+ /-- betadog (7)
| | | /-+
| | | | \-- betarabbi (8)
| | \--------+
| | \----- betakanga (9)
\-------------------+
| /- globinlam (10)
| /--------------+
| | \-- globinsea (11)
\-----+
| /------------------------- globinsoy (12)
\------------+
\---------------------- globinins (13)
|--------------| 0.500 expected changes per site
Calculating tree probabilities...
Credible sets of trees (194 trees sampled):
50 % credible set contains 4 trees
90 % credible set contains 28 trees
95 % credible set contains 47 trees
99 % credible set contains 109 trees
MrBayes >