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:
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:
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.
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}
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.
badger@badger.duq.edu