Differences

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

--- documentation [2013/06/03 12:58]
mmarcet created
+++ documentation [2013/06/03 13:15] (current)
mmarcet
@@ Line 2: / Line 2: @@
 //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:\\
-\\ Subtree reconstruction (**st**)\\ [[algorithm_tc|Tree comparison]] (**tc**)\\ [[algorithm_ps|Phylome support]] (**ps**) \\ [[algorithm_rd|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:**\\
@@ Line 45: / Line 45: @@
   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
+----
+  * [[start|Starting page]]
+  * [[Algorithm|Algorithm]]
+  * [[inputfiles|Input Files]]
+  * [[output | Output Files]]
+  * [[configuration_file | Configuration File]]
+  * [[downloads|Downloads]]
+  * [[about | About]]

TreeKo