The program chart
creates a chart that makes it easy to
compare the list of common clades from several runs. To create a chart,
use the command:
chart <file1> <file2> ...
where the files given are the ones created by the summarize
program. The result
is a list of all the clades the appear in a common clade table of any
of the input files, one per line. Each line also has a list of the
frequencies with which the clade occurs in each of the runs. To the
right of each line may be a list of asterisks. Each asterisk indicates
a 5% difference between the minimum and maximum values of the
frequencies. Here is a sample chart from the final runs on the Campanulaceae dataset.
{1-13} 1.000 1.000 1.000 1.000 1.000
{1-12} 1.000 1.000 1.000 1.000 1.000
{1-11} 0.289 0.277 0.291 0.289 0.293
{1-9,12} 0.231 0.255 0.223 0.257 0.250
{1-9} 1.000 1.000 1.000 1.000 1.000
{1-5,7-9} 0.455 0.388 0.379 0.398 0.347 **
{1-5,8-9} 0.203 0.161 0.177 0.183 0.134 *
{1-4,8-9} 0.943 0.906 0.875 0.907 0.799 **
{1-4} 0.195 0.185 0.182 0.195 0.173
{1-3,8-9} 0.190 0.178 0.172 0.187 0.172
{1-3} 0.182 0.185 0.184 0.207 0.193
{1,4-9} 0.013 0.013 0.025 0.015 0.037
{1,4,8-9} 0.188 0.185 0.179 0.184 0.161
{1,4} 0.186 0.204 0.188 0.191 0.191
{1,5-7} 0.013 0.017 0.025 0.013 0.038
{1,8-9} 0.179 0.173 0.195 0.215 0.171
{2-4,8-9} 0.205 0.197 0.183 0.170 0.171
{2-4} 0.199 0.199 0.197 0.199 0.194
{2-3,5-7} 0.011 0.014 0.017 0.000 0.037
{2-3,8-9} 0.195 0.204 0.186 0.183 0.184
{2-3} 0.995 0.997 0.991 0.997 0.992
{4,8-9} 0.223 0.193 0.199 0.179 0.186
{5-7} 0.495 0.574 0.578 0.555 0.615 **
{5,7} 0.715 0.691 0.644 0.692 0.577 **
{6-7} 0.130 0.185 0.222 0.172 0.325 ***
{8-9} 1.000 1.000 1.000 1.000 1.000
{10-12} 0.480 0.469 0.486 0.454 0.457
{10-11} 1.000 1.000 1.000 1.000 1.000
{1-7} 0.000 0.023 0.025 0.017 0.037
{1-3,5-9} 0.000 0.014 0.017 0.013 0.032
{1-3,5-7} 0.000 0.012 0.013 0.000 0.027
{2-9} 0.000 0.011 0.016 0.013 0.038
{2-3,5-9} 0.000 0.015 0.013 0.000 0.019
{4-7} 0.000 0.015 0.024 0.017 0.027
{5-9} 0.000 0.019 0.018 0.022 0.032
{1,4-7} 0.000 0.000 0.019 0.011 0.022
{2-7} 0.000 0.000 0.015 0.000 0.016
{4-9} 0.000 0.000 0.013 0.000 0.025
{1,5-9} 0.000 0.000 0.000 0.015 0.016
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badger@badger.duq.edu