User Tools

Site Tools


output

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

output [2013/06/03 13:16]
mmarcet
output [2013/06/03 13:17] (current)
mmarcet
Line 1: Line 1:
-=== Tree comparison output file ===+===== Tree comparison output file =====
  
 The information provided by the output can vary depending on the options enabled in the configuration file. Here we provide an example of the default output: The information provided by the output can vary depending on the options enabled in the configuration file. Here we provide an example of the default output:
Line 6: Line 6:
 The first part will show the configuration regarding the configuration options used in order to run the tree comparison program. Following that are the names of the tree files used and the number of pruned trees each original tree has. Then the two distances calculated by treeKO are provided. Lastly the list of pruned trees for each original tree is added. The information provided in the output can be modified using the configuration file. For more information,​ [[configuration_file|check this link]]. The first part will show the configuration regarding the configuration options used in order to run the tree comparison program. Following that are the names of the tree files used and the number of pruned trees each original tree has. Then the two distances calculated by treeKO are provided. Lastly the list of pruned trees for each original tree is added. The information provided in the output can be modified using the configuration file. For more information,​ [[configuration_file|check this link]].
  
-=== Reconciliation distance ===+===== Reconciliation distance ​=====
  
 A similar output file will be provided when using the tree reconciliation distances. For instance: A similar output file will be provided when using the tree reconciliation distances. For instance:
Line 16: Line 16:
  
  
-=== Tree comparison summarized result ===+===== Tree comparison summarized result ​=====
  
 For an easier parsing, the print_oneline option can be used in the configuration file. This option will output the speciation and strict distances in one line in the following format (results are tab delimited): For an easier parsing, the print_oneline option can be used in the configuration file. This option will output the speciation and strict distances in one line in the following format (results are tab delimited):
Line 25: Line 25:
   ​   ​
   ​   ​
-=== Phylome support output files ===+===== Phylome support output files =====
  
 The phylome support program provides three output files. The first one is a .pdf file where the species tree has been drawn. At each branch the phylome support value is represented. Next to it, in brackets, the bootstrap support (if present) is represented. Branch lengths in this tree are distorted and should not be taken into account. The newick file corresponding to the tree is provided in a second file, by default called species_tree.nw. Branch lengths represent the bootstrap support while the phylome support is represented as a bootstrap value. The phylome support program provides three output files. The first one is a .pdf file where the species tree has been drawn. At each branch the phylome support value is represented. Next to it, in brackets, the bootstrap support (if present) is represented. Branch lengths in this tree are distorted and should not be taken into account. The newick file corresponding to the tree is provided in a second file, by default called species_tree.nw. Branch lengths represent the bootstrap support while the phylome support is represented as a bootstrap value.
output.1370258196.txt.gz ยท Last modified: 2013/06/03 13:16 by mmarcet