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 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, check this link.

A similar output file will be provided when using the tree reconciliation distances. For instance:

Number of duplications: 2 Total number of events (duplication + loss): 8

These results show that two duplication events were recorded and a total of 8 events were detected (therefore the remaining 6 will be nodes that have been lost)

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):

 Tree 1 Tree 2 Strict distance Evolutionary distance ---------------------------------------------------------------------------- Results file_name1 file_name2 0.864 0.651

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.

For instance for the node represented in this figure:

The second file represents the statistics calculated during the phylome support calculation. For each node the alternative topologies considered are represented. For this particular tree the alternative topologies for node X would be represented as follows:

Topology found in the tree: A|B C Alternative topology 1: A|C B Alternative topology 2: C|B A 

The pipe symbol (“|”) divides the groups of species found in the most external node while a space divides the scaled, internal divisions. When a grandchild consists of more than one species, these species are separated by a dash (”-”). The output file for the phylome support statistics will represent for each line one alternative topology as explained above, followed by the number of trees that support that distribution and the percentage of trees this represents. For instance if we had 100 gene trees we could obtain a result such as this one:

A|B C 65 0.65 A|C B 20 0.20 B|C A 15 0.15