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:

Reconstruction of pruned trees (st)
Tree comparison (tc)
Phylome support (ps)
Reconciliation distance (rd)

Tree comparison:
To run the tree comparison program only two files are needed. The first file will always contain one single tree, it can be regarded as the reference tree. The second file can contain one single tree (-b option) in which case the reference tree and the second tree can be interchanged without changing the results:

python treeKO.py -a tree_file_1 -b tree_file_2 -p tc

Both Tree files should contain one single newick formatted tree. If more trees are provided in one single file they will be ignored. Species names need to match in the two trees, even though protein identification (if present) does not need to be the same.

Additionally, the second tree file can contain a list of tree files. In this case all the trees in the list will be compared to the reference tree.

python treeKO.py -a tree_file_1 -l list_trees -p tc

In the tree comparison program the list of trees can contain the seed protein code from which the tree was reconstructed. This seed can be used to filter the pruned trees so that only pruned trees that contain the seed will be used, this option can be activated with the -f option. Notice that the seed filter will only be applied to the list of trees. To filter the reference tree the seed will be provided by the configuration file:

python treeKO.py -a tree_file_1 -l list_trees -p tc -f True

The results of the tree comparison program will appear on screen unless a different output file is provided. The output file can be assigned with the -o parameter

python treeKO.py -a tree_file_1 -b tree_file_2 -o output_file_name -p tc

Additionally if the user only wishes to obtain the list of subtrees generated by treeKO for other purposes the st option can be used. The user can either provide a single tree (-a option) or a list of trees (-l option)

Reconciliation distance:

The reconciliation distance can be used in the same way as the tree comparison algorithm, just by substituting the program by rd:

python treeKO.py -a species_tree -b tree_file -o output_file_name -p rd

Take notice that the first tree has to be a species tree and that as such is not allowed to contain duplications. Additionally we recommend that you provide a rooted tree as the rooting will influence the final result.

Phylome support:

To calculate the phylome support a species tree should be supplied. Additionally a list of trees needs to be supplied.

python treeKO.py -a species_tree_file -l list_trees -p ps

The species_tree_file should contain one single, rooted, tree. The partitions used to calculate the phylome support are derived automatically from the species tree therefore this tree needs to be rooted by the user, else unexpected or unwanted partitions may be considered.

A list of trees or tree paths also needs to be supplied. In this instance the name of the seed used to construct the tree also needs to be provided. The format accepted by treeKO is a tab delimited file in which each line represents a tree (or tree path): seed <tab> tree path.

Just as the tree comparison program, the phylome support program can print its results on-screen or in an outputting file (-o option). Additionally phylome support has two more outfiles where the species tree with phylome support will be printed. If no values are provided for the -t and -n options, the species tree will be printed in the default files: species_tree.pdf and species_tree.nw.

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