BADGER

Bayesian Analysis to Describe Genomic Evolution by Rearrangement

Version 1.02 beta, June 11, 2004

Comparing common clade lists

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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