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documentation [2013/06/03 13:03] mmarcet |
documentation [2013/06/03 13:15] (current) mmarcet |
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//All the files downloaded in the treeKO package need to be in the same directory for the program to work//\\ | //All the files downloaded in the treeKO package need to be in the same directory for the program to work//\\ | ||
To run treeKO on default parameters a program needs to be chosen using the **-p** option:\\ | To run treeKO on default parameters a program needs to be chosen using the **-p** option:\\ | ||
- | \\ Subtree reconstruction (**st**)\\ [[algorithm_tc|Tree comparison]] (**tc**)\\ [[algorithm#phylome_support_algorithm|Phylome support]] (**ps**) \\ [[algorithm#reconciliation_distance|Reconciliation distance]] (**rd**) | + | \\ [[algorithm#reconstruction_of_pruned_trees|Reconstruction of pruned trees]] (**st**)\\ [[algorithm#tree_comparison_algorithm|Tree comparison]] (**tc**)\\ [[algorithm#phylome_support_algorithm|Phylome support]] (**ps**) \\ [[algorithm#reconciliation_distance|Reconciliation distance]] (**rd**) |
**Tree comparison:**\\ | **Tree comparison:**\\ | ||
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python treeKO.py -a species_tree_file -l list_trees -p ps -o statistics_outfile -t species_tree_outfile.pdf -n species_tree_newick_outfile | python treeKO.py -a species_tree_file -l list_trees -p ps -o statistics_outfile -t species_tree_outfile.pdf -n species_tree_newick_outfile | ||
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+ | ---- | ||
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+ | * [[start|Starting page]] | ||
+ | * [[Algorithm|Algorithm]] | ||
+ | * [[inputfiles|Input Files]] | ||
+ | * [[output | Output Files]] | ||
+ | * [[configuration_file | Configuration File]] | ||
+ | * [[downloads|Downloads]] | ||
+ | * [[about | About]] | ||
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