BADGER

Bayesian Analysis to Describe Genomic Evolution by Rearrangement

Version 1.02 beta, June 11, 2004

Copyright © 2004 by Bret Larget & Don Simon


Summarizing output files


The program summarize acts on a tree topology (.top) file generated by the badger program. It counts the appearance of each tree topology, automatically identifies clades, displays the frequency each tree topology appears, shows transitions between subtree topologies within clades, and lists the common clades.

We define a named clade with these criteria:

  1. A named clade must have at least two members.
  2. The members of a named clade must appear as a monophyletic group in at least a proportion named_clade_threshold of all sampled tree topologies. The threshold must be greater than one half.
  3. There may not be more than max_top different subtree topologies among all sampled trees where the named clade is monophyletic.
  4. A named clade cannot be a proper subset of another named clade.

These rules for naming clades give the user some flexibility and make reading summaries of the posterior for large trees substantially easier.

The options for summarize are:

Summarize Options
Option Description
-s Number of lines to skip from each input file. 0 is the default.
-t Number of trees to print. 100 is the default. 0 means print all trees.
-c Threshold for an arbitrary clade to be printed. 0.01 is the default.
-p Threshold for named clade definition (must be greater than .5). 0.8 is the default.
-m Maximum number of subtree topologies within a named clade. 100 is the default.

The most general way to call summarize is:

summarize [-h] [--help]
 [-s skipped_lines] [--skip skipped_lines]
 [-t number_of_trees_to_print] [--trees number_of_trees_to_print]
 [-c threshold_for_clades] [--cthreshold threshold_for_clades]
 [-n threshold_for_named_clades] [--nthreshold threshold_for_named_clades]
 [-m max_tree_topologies] [--maxtopologies max_tree_topologies]
 <file1>  <file2> ...

The square brackets indicate optional arguments. If the symbol `-' is used in place of a file name, the program expects the input from standard input.

Examples

summarize -s 200 -n .8 -m 8 run1.top run2.top run3.top > runs.sum

will ignore the first 200 input lines from each file and summarize the concatenation of the remaining files with named clades having a threshold of 80% and no more than eight subtree topologies observed in the combined sample.

head -20000 run1.top | tail -10000 | summarize - > run1.sum

will run summarize on lines 10,001 through 20,000 of run1.top.

The summarize program output contains several components. The example used below is from a .top file from the last run of the example runs for Campanulaceae dataset. There are 13 taxa in this example. The command to generate this output was:

summarize -s 100 camp.run1.0.top

The first section of the summary output shows the classification of taxa into named clades and how often each named clade and subtree topology appears. Taxa that do not appear in a named clade are listed separately.


******************** Named clades ********************

  1415  A    {1-4,8-9}
   123  A1   (1,((2,3),(4,(8,9))))
   115  A2   ((1,(4,(8,9))),(2,3))
   114  A3   ((1,((2,3),4)),(8,9))
    97  A4   (((1,(2,3)),(8,9)),4)
    95  A5   ((1,((2,3),(8,9))),4)
    94  A6   (1,(((2,3),(8,9)),4))
    92  A7   ((1,(8,9)),((2,3),4))
    91  A8   ((1,4),((2,3),(8,9)))
    91  A9   (((1,4),(2,3)),(8,9))
    88  A10  ((1,(2,3)),(4,(8,9)))
    87  A11  (((1,4),(8,9)),(2,3))
    87  A12  (((1,(8,9)),(2,3)),4)
    82  A13  (((1,(2,3)),4),(8,9))
    78  A14  (1,(((2,3),4),(8,9)))
    74  A15  (((1,(8,9)),4),(2,3))
     1  A16  (1,(((2,4),3),(8,9)))
     1  A17  (1,(((2,(8,9)),3),4))
     1  A18  (1,(((2,(8,9)),4),3))
     1  A19  ((1,(2,(3,(8,9)))),4)
     1  A20  ((1,(3,(4,(8,9)))),2)
     1  A21  ((1,((2,(8,9)),3)),4)
     1  A22  (((1,2),(8,9)),(3,4))

  1500  B    {10-11}
  1500  B1   (10,11)

              5
              6
              7
             12
             13


The next section of summary output gives a complete sorted list of each observed tree topology. The file lists the 100 most common trees printing out the clades names for the named clades. The first column is the raw count. The second column is the posterior probability of the tree topology. The third column is the cumulative posterior probability. Notice that the posterior probabilities for the trees are fairly even, with no clear "best" tree. You must refer back to the named clades for a complete description.


******************** Tree topologies ********************

Count  Prob.  Cum.  Tree topology
   33  0.022  0.022 (((A1,((5,7),6)),(B1,12)),13)
   29  0.019  0.041 (((A2,((5,7),6)),(B1,12)),13)
   27  0.018  0.059 (((A3,((5,7),6)),(B1,12)),13)
   21  0.014  0.073 ((((A10,(5,7)),6),(B1,12)),13)
   21  0.014  0.087 (((A4,((5,7),6)),(B1,12)),13)
   20  0.013  0.101 (((A6,((5,7),6)),(B1,12)),13)
   20  0.013  0.114 ((((A1,(5,7)),6),(B1,12)),13)
   20  0.013  0.127 (((A5,((5,7),6)),(B1,12)),13)
   20  0.013  0.141 (((A9,((5,7),6)),(B1,12)),13)
   20  0.013  0.154 (((A11,((5,7),6)),(B1,12)),13)
   20  0.013  0.167 ((((A3,(5,7)),6),(B1,12)),13)
   19  0.013  0.180 (((A7,((5,7),6)),(B1,12)),13)
   19  0.013  0.193 ((((A1,((5,7),6)),B1),12),13)
   19  0.013  0.205 ((((A2,(5,7)),6),(B1,12)),13)
   18  0.012  0.217 (((A13,((5,7),6)),(B1,12)),13)
   17  0.011  0.229 (((A10,((5,7),6)),(B1,12)),13)
   17  0.011  0.240 ((((A6,(5,7)),6),(B1,12)),13)
   16  0.011  0.251 ((((A8,((5,7),6)),B1),12),13)
   16  0.011  0.261 ((((A2,((5,7),6)),B1),12),13)
   16  0.011  0.272 ((((A12,((5,7),6)),B1),12),13)
   15  0.010  0.282 ((((A7,((5,7),6)),B1),12),13)
   15  0.010  0.292 ((((A11,((5,7),6)),B1),12),13)
   14  0.009  0.301 (((A14,((5,7),6)),(B1,12)),13)
   14  0.009  0.311 (((A8,((5,7),6)),(B1,12)),13)
   14  0.009  0.320 ((((A5,(5,7)),6),(B1,12)),13)
   14  0.009  0.329 ((((A5,((5,7),6)),B1),12),13)
   14  0.009  0.339 ((((A13,((5,7),6)),B1),12),13)
   14  0.009  0.348 (((((A2,(5,7)),6),B1),12),13)
   14  0.009  0.357 ((((A12,(5,7)),6),(B1,12)),13)
   14  0.009  0.367 ((((A12,((5,7),6)),12),B1),13)
   14  0.009  0.376 (((((A5,(5,7)),6),B1),12),13)
   13  0.009  0.385 ((((A8,(5,7)),6),(B1,12)),13)
   13  0.009  0.393 (((A12,((5,7),6)),(B1,12)),13)
   13  0.009  0.402 (((((A6,(5,7)),6),B1),12),13)
   13  0.009  0.411 ((((A9,((5,7),6)),B1),12),13)
   12  0.008  0.419 ((((A10,((5,7),6)),B1),12),13)
   12  0.008  0.427 ((((A4,(5,7)),6),(B1,12)),13)
   12  0.008  0.435 ((((A4,((5,7),6)),B1),12),13)
   12  0.008  0.443 ((((A15,(5,7)),6),(B1,12)),13)
   12  0.008  0.451 ((((A15,((5,7),6)),B1),12),13)
   12  0.008  0.459 (((((A3,5),7),6),(B1,12)),13)
   11  0.007  0.466 ((((A14,((5,7),6)),12),B1),13)
   11  0.007  0.473 ((((A6,((5,7),6)),12),B1),13)
   11  0.007  0.481 ((((A3,((5,7),6)),B1),12),13)
   11  0.007  0.488 ((((A13,(5,7)),6),(B1,12)),13)
   11  0.007  0.495 (((((A7,(5,7)),6),12),B1),13)
   11  0.007  0.503 (((((A9,(5,7)),6),B1),12),13)
   11  0.007  0.510 ((((((A4,5),7),6),12),B1),13)
   10  0.007  0.517 ((((A1,((5,7),6)),12),B1),13)
   10  0.007  0.523 (((A15,((5,7),6)),(B1,12)),13)
   10  0.007  0.530 (((((A1,5),7),6),(B1,12)),13)
   10  0.007  0.537 ((((A9,(5,7)),6),(B1,12)),13)
   10  0.007  0.543 ((((A11,(5,7)),6),(B1,12)),13)
   10  0.007  0.550 (((((A11,(5,7)),6),B1),12),13)
   10  0.007  0.557 (((((A4,(5,7)),6),12),B1),13)
    9  0.006  0.563 (((((A1,(5,7)),6),12),B1),13)
    9  0.006  0.569 (((((A14,(5,7)),6),12),B1),13)
    9  0.006  0.575 (((((A14,(5,7)),6),B1),12),13)
    9  0.006  0.581 (((((A8,5),7),6),(B1,12)),13)
    9  0.006  0.587 (((((A8,(5,7)),6),12),B1),13)
    9  0.006  0.593 (((((A7,5),7),6),(B1,12)),13)
    9  0.006  0.599 (((((A7,(5,7)),6),B1),12),13)
    9  0.006  0.605 (((((A3,(5,7)),6),12),B1),13)
    9  0.006  0.611 (((((A5,5),7),6),(B1,12)),13)
    9  0.006  0.617 (((((A9,(5,7)),6),12),B1),13)
    9  0.006  0.623 (((((A4,5),7),6),(B1,12)),13)
    9  0.006  0.629 (((((A15,5),7),6),(B1,12)),13)
    8  0.005  0.634 ((((A14,(5,7)),6),(B1,12)),13)
    8  0.005  0.639 ((((A10,((5,7),6)),12),B1),13)
    8  0.005  0.645 ((((A2,((5,7),6)),12),B1),13)
    8  0.005  0.650 ((((A3,((5,7),6)),12),B1),13)
    8  0.005  0.655 (((((A14,5),7),6),(B1,12)),13)
    8  0.005  0.661 ((((A9,((5,7),6)),12),B1),13)
    8  0.005  0.666 ((((A11,((5,7),6)),12),B1),13)
    8  0.005  0.671 (((((A3,(5,7)),6),B1),12),13)
    8  0.005  0.677 (((((A5,(5,7)),6),12),B1),13)
    8  0.005  0.682 (((((A13,5),7),6),(B1,12)),13)
    7  0.005  0.687 ((((A6,((5,7),6)),B1),12),13)
    7  0.005  0.691 ((((A7,(5,7)),6),(B1,12)),13)
    7  0.005  0.696 ((((A7,((5,7),6)),12),B1),13)
    7  0.005  0.701 (((((A1,(5,7)),6),B1),12),13)
    7  0.005  0.705 ((((A5,((5,7),6)),12),B1),13)
    7  0.005  0.710 ((((A13,((5,7),6)),12),B1),13)
    7  0.005  0.715 (((((A10,(5,7)),6),12),B1),13)
    7  0.005  0.719 ((((A4,((5,7),6)),12),B1),13)
    7  0.005  0.724 ((((A15,((5,7),6)),12),B1),13)
    7  0.005  0.729 (((((A11,(5,7)),6),12),B1),13)
    7  0.005  0.733 (((((A4,(5,7)),6),B1),12),13)
    7  0.005  0.738 ((((((A7,5),7),6),B1),12),13)
    7  0.005  0.743 ((((((A11,5),7),6),12),B1),13)
    6  0.004  0.747 ((((A14,((5,7),6)),B1),12),13)
    6  0.004  0.751 (((((A6,5),7),6),(B1,12)),13)
    6  0.004  0.755 (((((A6,(5,7)),6),12),B1),13)
    6  0.004  0.759 (((((A8,(5,7)),6),B1),12),13)
    6  0.004  0.763 (((((A10,5),7),6),(B1,12)),13)
    6  0.004  0.767 (((((A2,(5,7)),6),12),B1),13)
    6  0.004  0.771 ((((((A1,5),7),6),B1),12),13)
    6  0.004  0.775 ((((((A8,5),7),6),B1),12),13)
    6  0.004  0.779 (((((A13,(5,7)),6),B1),12),13)
    6  0.004  0.783 (((((A15,(5,7)),6),12),B1),13)


The next section of summary output is similar to bootstrap proportions given by other methods. Relative to the most probable tree topology, the posterior probability of every clade, named or not, that occurs in at least 1% of the trees is provided.


***** Posterior probabilities of clades in most probable tree topology *****

     Count  Prob. Tree topology
      1500  1.000 {1-13}
      1500  1.000 {1-12}
      1500  1.000 {1-9}
      1500  1.000 {8-9}
      1500  1.000 {10-11}
      1415  0.943 {1-4,8-9}
       683  0.455 {1-5,7-9}
       347  0.231 {1-9,12}
       305  0.203 {1-5,8-9}
       292  0.195 {2-3,8-9}
       285  0.190 {1-3,8-9}

For each named clade we summarize the transitions between subtree topologies. These tables can be useful for examining mixing efficiency. Ideally, the transitions would occur as frequently as one might expect from independent samples from the posterior, but this is almost never approached. It is important that there be a sufficient number of transitions between various likely subtree topologies.


******************** Clade transition matrices ********************

    |  A1   A2   A3   A4   A5   A6   A7   A8   A9   A10  A11  A12  A13  A14  A15  A16  A17  A18  A19  A20  A21  A22   -  
----+-------------------------------------------------------------------------------------------------------------------
 A1 |  11    8   12    8   10   10   14    9    3    7    5    7    8    7    3    0    0    0    0    0    0    0    1 
 A2 |   8    7    9    9    7    8   11    6    5    6    9    8    5    6    6    0    0    1    0    0    0    1    3 
 A3 |   5    7   11    3   12    4    8    5   11    5    4    6   10    9    7    1    0    0    0    0    0    0    6 
 A4 |   6    8   10    5    4    6    7    6    9    6    9    4    7    4    5    0    0    0    0    0    0    0    1 
 A5 |   8   13   11    4    6    4    3    7   10    3    5    3    6    5    7    0    0    0    0    0    0    0    0 
 A6 |   7   10    3    6    2    9    2    5    5    6   11    9    2    7    9    0    0    0    0    0    0    0    1 
 A7 |   9   11   12    7    4    6    2    5    5    8    2    6    4    3    7    0    0    0    0    0    1    0    0 
 A8 |   9    5    6    5    4    6   10    8    2    6   11    3    2    7    4    0    0    0    0    1    0    0    2 
 A9 |  10    6    5    4    7    6    5    6    7    9    5    4    8    5    3    0    0    0    0    0    0    0    1 
 A10|   9   12    6   11    5    6    4    5    6    3    3    5    5    1    5    0    0    0    0    0    0    0    2 
 A11|  11    2    1   14    5    7    2    6    6    8    7    3    5    6    4    0    0    0    0    0    0    0    0 
 A12|   8    6    3    6    4    7    7    6    6    3    7    7    4    5    5    0    0    0    0    0    0    0    3 
 A13|   6    7    6    8    8    6    4    7    3    3    5    7    5    4    2    0    0    0    0    0    0    0    0 
 A14|   6    7    6    4   12    3    3    5    6    6    2    5    6    4    2    0    0    0    0    0    0    0    1 
 A15|  10    5    6    1    4    4    8    3    4    6    2    7    3    4    4    0    1    0    1    0    0    0    1 
 A16|   0    0    0    0    0    0    0    0    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
 A17|   0    0    0    0    0    0    0    0    0    1    0    0    0    0    0    0    0    0    0    0    0    0    0 
 A18|   0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    1 
 A19|   0    0    0    0    0    0    0    0    0    0    0    1    0    0    0    0    0    0    0    0    0    0    0 
 A20|   0    0    0    0    0    0    0    0    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
 A21|   0    0    0    0    0    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
 A22|   0    0    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
  - |   0    1    6    2    0    1    2    2    1    2    0    2    2    1    1    0    0    0    0    0    0    0   62 


    |  B1  
----+-----
 B1 | 1499 

The next portion of the summary output shows "clade trees" where the subtree topology differences within named clades is ignored.


******************** Clade tree topologies ********************

Count  Prob.  Cum.  Tree topology
  298  0.199  0.199 (((A,((5,7),6)),(B,12)),13)
  208  0.139  0.337 ((((A,(5,7)),6),(B,12)),13)
  198  0.132  0.469 ((((A,((5,7),6)),B),12),13)
  129  0.086  0.555 (((((A,(5,7)),6),B),12),13)
  125  0.083  0.639 ((((A,((5,7),6)),12),B),13)
  114  0.076  0.715 (((((A,(5,7)),6),12),B),13)
  113  0.075  0.790 (((((A,5),7),6),(B,12)),13)
   61  0.041  0.831 ((((((A,5),7),6),12),B),13)
   58  0.039  0.869 ((((((A,5),7),6),B),12),13)
   29  0.019  0.889 ((((A,5),(6,7)),(B,12)),13)
   24  0.016  0.905 (((A,(5,(6,7))),(B,12)),13)
   24  0.016  0.921 (((((A,5),(6,7)),12),B),13)
   20  0.013  0.934 (((((A,5),(6,7)),B),12),13)
    8  0.005  0.939 ((((A,(5,(6,7))),12),B),13)
    5  0.003  0.943 ((((A,(5,(6,7))),B),12),13)
    3  0.002  0.945 ((((1,(5,(6,7))),(((2,3),(8,9)),4)),(B,12)),13)
    3  0.002  0.947 (((((1,(5,(6,7))),(8,9)),((2,3),4)),(B,12)),13)
    2  0.001  0.948 (((1,((((2,3),4),(8,9)),(5,(6,7)))),(B,12)),13)
    2  0.001  0.949 ((((1,(5,(6,7))),(((2,3),4),(8,9))),(B,12)),13)
    2  0.001  0.951 ((((1,(8,9)),(((2,3),(5,(6,7))),4)),(B,12)),13)
    2  0.001  0.952 ((((1,((2,3),((5,(6,7)),(8,9)))),4),(B,12)),13)
    2  0.001  0.953 ((((1,(((2,3),(5,(6,7))),4)),(8,9)),(B,12)),13)
    2  0.001  0.955 (((((1,(8,9)),4),((2,3),(5,(6,7)))),(B,12)),13)
    2  0.001  0.956 (((((1,(8,9)),(4,(5,(6,7)))),(2,3)),(B,12)),13)
    2  0.001  0.957 (((((1,((4,(5,(6,7))),(8,9))),(2,3)),12),B),13)
    2  0.001  0.959 (((((1,(((2,3),(8,9)),(5,(6,7)))),4),B),12),13)
    2  0.001  0.960 ((((((1,4),((2,3),(5,(6,7)))),(8,9)),B),12),13)
    2  0.001  0.961 ((((((1,(5,(6,7))),(8,9)),4),(2,3)),(B,12)),13)
    2  0.001  0.963 ((((((1,(8,9)),(5,(6,7))),(2,3)),4),(B,12)),13)
    1  0.001  0.963 (((1,(((2,3),(4,(5,(6,7)))),(8,9))),(B,12)),13)
    1  0.001  0.964 (((1,((((2,3),(5,(6,7))),(8,9)),4)),(B,12)),13)
    1  0.001  0.965 (((1,((((2,3),(8,9)),4),(5,(6,7)))),(B,12)),13)
    1  0.001  0.965 ((((1,4),(((2,3),(8,9)),(5,(6,7)))),(B,12)),13)
    1  0.001  0.966 ((((1,(2,3)),((4,(8,9)),(5,(6,7)))),(B,12)),13)
    1  0.001  0.967 ((((1,((2,3),4)),((5,(6,7)),(8,9))),(B,12)),13)
    1  0.001  0.967 ((((1,((2,3),(4,(5,(6,7))))),(8,9)),(B,12)),13)
    1  0.001  0.968 ((((1,((2,3),(4,((5,(6,7)),(8,9))))),B),12),13)
    1  0.001  0.969 ((((1,((4,(8,9)),(5,(6,7)))),(2,3)),(B,12)),13)
    1  0.001  0.969 ((((1,(((2,3),4),((5,(6,7)),(8,9)))),12),B),13)
    1  0.001  0.970 ((((1,(((2,3),(4,(5,(6,7)))),(8,9))),B),12),13)
    1  0.001  0.971 ((((1,(((2,3),(4,(8,9))),(5,(6,7)))),12),B),13)
    1  0.001  0.971 ((((1,(((2,3),(5,(6,7))),(4,(8,9)))),B),12),13)
    1  0.001  0.972 ((((1,(((2,3),((5,(6,7)),(8,9))),4)),B),12),13)
    1  0.001  0.973 ((((1,((((2,3),(5,(6,7))),4),(8,9))),12),B),13)
    1  0.001  0.973 ((((1,((((2,3),(5,(6,7))),4),(8,9))),B),12),13)
    1  0.001  0.974 ((((1,((((2,3),(8,9)),(5,(6,7))),4)),B),12),13)
    1  0.001  0.975 (((((1,4),(2,3)),((5,(6,7)),(8,9))),(B,12)),13)
    1  0.001  0.975 (((((1,4),(8,9)),((2,3),(5,(6,7)))),(B,12)),13)
    1  0.001  0.976 (((((1,(2,3)),(8,9)),(4,(5,(6,7)))),(B,12)),13)
    1  0.001  0.977 (((((1,(2,3)),((5,(6,7)),(8,9))),4),(B,12)),13)
    1  0.001  0.977 (((((1,(4,(5,(6,7)))),(8,9)),(2,3)),(B,12)),13)
    1  0.001  0.978 (((((1,(4,(8,9))),(5,(6,7))),(2,3)),(B,12)),13)
    1  0.001  0.979 (((((1,(5,(6,7))),4),((2,3),(8,9))),(B,12)),13)
    1  0.001  0.979 (((((1,(5,(6,7))),(2,3)),(4,(8,9))),(B,12)),13)
    1  0.001  0.980 (((((1,(8,9)),(2,3)),(4,(5,(6,7)))),(B,12)),13)
    1  0.001  0.981 (((((1,(8,9)),(((2,3),4),(5,(6,7)))),B),12),13)
    1  0.001  0.981 (((((1,((2,3),(4,(5,(6,7))))),(8,9)),12),B),13)
    1  0.001  0.982 (((((1,((5,(6,7)),(8,9))),4),(2,3)),(B,12)),13)
    1  0.001  0.983 (((((1,(((2,3),(5,(6,7))),4)),(8,9)),B),12),13)
    1  0.001  0.983 ((((((1,4),(2,3)),((5,(6,7)),(8,9))),12),B),13)
    1  0.001  0.984 ((((((1,4),(8,9)),((2,3),(5,(6,7)))),12),B),13)
    1  0.001  0.985 ((((((1,4),((2,3),(5,(6,7)))),(8,9)),12),B),13)
    1  0.001  0.985 ((((((1,4),((2,(5,(6,7))),3)),(8,9)),B),12),13)
    1  0.001  0.986 ((((((1,(2,3)),(5,(6,7))),4),(8,9)),(B,12)),13)
    1  0.001  0.987 ((((((1,(2,3)),(8,9)),(4,(5,(6,7)))),12),B),13)
    1  0.001  0.987 ((((((1,(4,(8,9))),(5,(6,7))),(2,3)),12),B),13)
    1  0.001  0.988 ((((((1,(5,(6,7))),4),(8,9)),(2,3)),(B,12)),13)
    1  0.001  0.989 ((((((1,(5,(6,7))),(2,3)),4),(8,9)),(B,12)),13)
    1  0.001  0.989 ((((((1,(5,(6,7))),(8,9)),(2,3)),4),(B,12)),13)
    1  0.001  0.990 ((((((1,(8,9)),(2,3)),(5,(6,7))),4),(B,12)),13)
    1  0.001  0.991 ((((((1,(8,9)),(4,(5,(6,7)))),(2,3)),B),12),13)
    1  0.001  0.991 ((((((1,(8,9)),(5,(6,7))),4),(2,3)),(B,12)),13)
    1  0.001  0.992 ((((((1,(8,9)),(5,(6,7))),((2,3),4)),12),B),13)
    1  0.001  0.993 ((((((1,((2,3),4)),(5,(6,7))),(8,9)),12),B),13)
    1  0.001  0.993 ((((((1,((2,3),4)),(5,(6,7))),(8,9)),B),12),13)
    1  0.001  0.994 (((((((1,4),(5,(6,7))),(8,9)),(2,3)),B),12),13)
    1  0.001  0.995 (((((((1,(2,3)),(5,(6,7))),(8,9)),4),B),12),13)
    1  0.001  0.995 (((((A,6),(5,7)),B),12),13)
    1  0.001  0.996 (((((((1,(5,(6,7))),4),(8,9)),(2,3)),12),B),13)
    1  0.001  0.997 (((((((1,(5,(6,7))),4),(8,9)),(2,3)),B),12),13)
    1  0.001  0.997 (((((((1,(5,(6,7))),(2,3)),(8,9)),4),B),12),13)
    1  0.001  0.998 (((((((1,(5,(6,7))),(8,9)),4),(2,3)),B),12),13)
    1  0.001  0.999 (((((((1,(5,(6,7))),(8,9)),(2,3)),4),B),12),13)
    1  0.001  0.999 (((((((1,(8,9)),(5,(6,7))),4),(2,3)),12),B),13)
    1  0.001  1.000 (((((((1,(8,9)),(5,(6,7))),4),(2,3)),B),12),13)

The last section lists the most common clades, whether named or not. These clades must occur at least a proportion clade_threshold of all sampled trees.


************************ Common Clades ************************

      1500  1.000 {1-13}
      1500  1.000 {1-12}
       433  0.289 {1-11}
       347  0.231 {1-9,12}
      1500  1.000 {1-9}
       683  0.455 {1-5,7-9}
       305  0.203 {1-5,8-9}
      1415  0.943 {1-4,8-9}
       292  0.195 {1-4}
       285  0.190 {1-3,8-9}
       273  0.182 {1-3}
        20  0.013 {1,4-9}
       282  0.188 {1,4,8-9}
       279  0.186 {1,4}
        20  0.013 {1,5-7}
       269  0.179 {1,8-9}
       307  0.205 {2-4,8-9}
       298  0.199 {2-4}
        17  0.011 {2-3,5-7}
       292  0.195 {2-3,8-9}
      1492  0.995 {2-3}
       334  0.223 {4,8-9}
       743  0.495 {5-7}
      1073  0.715 {5,7}
       195  0.130 {6-7}
      1500  1.000 {8-9}
       720  0.480 {10-12}
      1500  1.000 {10-11}

After performing several runs and summarizing the results, the chart program may be used to create a comparison chart of the lists of common clades. Such a chart makes it easy to see how well the different runs agree.

Back to the table of contents.


This page was most recently updated on June 29, 2004.

badger@badger.duq.edu