http://treeko.cgenomics.org/ 2012-05-20T19:43:14+02:00 http://treeko.cgenomics.org/ http://treeko.cgenomics.org/lib/images/favicon.ico text/html 2012-03-22T15:10:17+02:00 Marina Marcet-Houben http://treeko.cgenomics.org/doku.php?id=downloads&rev=1332425417&do=diff TreeKO dependencies TreeKO is a python script that is implemented in the ETE <http://ete.cgenomics.org> programming toolkit. For it to work, ETE needs to be installed. ETE can be downloaded from here, an installation guide is also provided in the same page. text/html 2011-05-16T14:53:14+02:00 Marina Marcet http://treeko.cgenomics.org/doku.php?id=about&rev=1305550394&do=diff TreeKO is developed at the Gabaldón's lab (<http://gabaldonlab.crg.es>) at the Centre for Genomic Regulation (Barcelona, Spain). Contact information: mmarcet [ at ] crg.es tgabaldon [ at ] crg.es Support For any question regarding the use of treeKO or to report bugs in the program, you can join our google group: text/html 2011-05-16T14:52:17+02:00 Marina Marcet http://treeko.cgenomics.org/doku.php?id=start&rev=1305550337&do=diff TreeKO TreeKO is a python package used to compare phylogenetic trees. Currently it contains two different programs: Tree comparison The tree comparison algorithm has been designed in order to be able to compare trees that have undergone gene loss and gene duplication processes and therefore do not necessarily have the same number of leaves. TreeKO computes all the possible pruned trees in each original tree by splitting the trees by the duplication nodes and reassembling the trees with combin… text/html 2011-01-18T10:17:20+02:00 Marina Marcet http://treeko.cgenomics.org/doku.php?id=documentation&rev=1295342240&do=diff Running treeKO on default parameters 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) Tree comparison (tc) Phylome support (ps) Reconciliation distance (rd) text/html 2011-01-17T13:17:56+02:00 Marina Marcet http://treeko.cgenomics.org/doku.php?id=algorithm_subtrees&rev=1295266676&do=diff Reconstruction of pruned trees: TreeKO divides the original trees in single gene pruned trees using the duplication nodes as points in which the tree can be split and re-assembled. ETE (REF) is used to root the tree by one of the methods implemented in treeKO and is used to predict all the duplication nodes present in the tree. TreeKO implements two methods in order to detect duplications nodes: species overlap and tree reconciliation. The user can also provide their own duplication annotation… text/html 2011-01-17T10:51:44+02:00 Marina Marcet http://treeko.cgenomics.org/doku.php?id=output_files&rev=1295257904&do=diff 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 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 … text/html 2011-01-12T14:37:24+02:00 Marina Marcet http://treeko.cgenomics.org/doku.php?id=configuration_file&rev=1294839444&do=diff Configuration file While TreeKo is able to run on default values, it is advisable to use a configuration file in order to adapt its use to the data. The configuration file can be used to change the rooting method, printing information or to limit the number of pruned trees allowed during the use of TreeKo. Lines starting with # will be regarded as comments. There are two kind of values in the configuration file. The True/False values consist in one tag which will enable/disable the option. For… text/html 2011-01-12T14:36:09+02:00 Marina Marcet http://treeko.cgenomics.org/doku.php?id=input_files&rev=1294839369&do=diff Input files accepted by treeKO Single tree file The main input of treeKO are trees in newick format. These trees can either be rooted or unrooted. If they are unrooted, the program will root the tree according to the rooting method that the user has selected in the configuration file or it will use the default method. Information regarding duplication and speciation nodes can be provided by the user using the extended newick format (NHX <http://phylosoft.org/NHX/>). In order to use it, each in… text/html 2011-01-12T11:52:47+02:00 Marina Marcet http://treeko.cgenomics.org/doku.php?id=sidebar&rev=1294829567&do=diff Overview: * Introduction * Algorithm * Reconstruction of pruned trees * Tree comparison * Phylome support * Reconciliation distance * How to run treeKO * Input files * Configuration file * Output files * Links of interest * About text/html 2010-11-24T12:53:53+02:00 Marina Marcet http://treeko.cgenomics.org/doku.php?id=algorithm_rd&rev=1290599633&do=diff Reconciliation distance The strict reconciliation between a gene tree and a species tree is calculated. For each incongruence between the species tree and the gene tree a duplication event is assumed with a subsequent number of losses. Two different distances are offered in this mode: Duplication distance and Reconciliation cost distance. In the first one only duplications are computed. In the second both, duplication and loss events are computed. Loss events are considered as nodes that have …