http://treeko.cgenomics.org/ 2012-05-20T19:43:39+02:00 http://treeko.cgenomics.org/ http://treeko.cgenomics.org/lib/images/favicon.ico text/html 2011-05-16T14:53:14+02:00 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 2010-06-10T10:38:53+02:00 http://treeko.cgenomics.org/doku.php?id=algorithm&rev=1276159133&do=diff TreeKO Algorithm The algorithm used by treeKO to compare trees can be summarized in the following graph: The subtree reconstruction part is common to both programs implemented in treeKO. Depending on the program chosen by the user, treeKO will compare two trees and provide several distance measures. Alternatively treeKO will compute the phylome support for a given species tree. text/html 2010-10-07T12:47:31+02:00 http://treeko.cgenomics.org/doku.php?id=algorithm_ps&rev=1286448451&do=diff Phylome Support algorithm The phylome support value for a node can be defined as the percentage of trees in a large collection of gene trees (for instance a phylome) that present exactly the same topological arrangement of the partitions defined by its two daughter nodes. text/html 2010-11-24T12:53:53+02:00 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 … text/html 2011-01-17T13:17:56+02:00 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 2010-10-07T12:25:29+02:00 http://treeko.cgenomics.org/doku.php?id=algorithm_tc&rev=1286447129&do=diff Tree Comparison algorithm Once the pruned trees for each input tree have been calculated the tree comparison program is able to compare them and calculate the distance that separates the two trees. Distance calculation: Distances, as calculated by the tree comparison program, are a modification of the Robinson & Foulds (RF) calculation and as such only take topology into account. Branch lengths are not considered for the final distance result. Two different distances can be obtained from th… text/html 2010-03-24T11:23:10+02:00 http://treeko.cgenomics.org/doku.php?id=citation&rev=1269426190&do=diff Citations If you use treeKo please cite: treeKo.cgenomics.org and Jaime Huerta-Cepas, Joaquín Dopazo and Toni Gabaldón. ETE: a python Environment for Tree Exploration. BMC Bioinformatics 2010, 11:24. text/html 2011-01-12T14:37:24+02:00 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 2011-01-18T10:17:20+02:00 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 2012-03-22T15:10:17+02:00 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 2011-01-12T14:36:09+02:00 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 2010-03-09T15:50:05+02:00 http://treeko.cgenomics.org/doku.php?id=interesting_links&rev=1268146205&do=diff Links of interest: * phylomeDB : <http://www.phylomedb.org> * ETE: <http://ete.cgenomics.org/> * Comparative genomics group: <http://gabaldonlab.crg.es> text/html 2010-03-10T09:22:36+02:00 http://treeko.cgenomics.org/doku.php?id=introduction&rev=1268209356&do=diff TreeKo TreeKo is a python program used to compare phylogenetic rooted trees. It has been designed in order to be able to deal with 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 subtrees in each original tree by splitting the trees by the duplication nodes and reassembling the trees with combinations of subtrees. Subtrees are then compared all against all, pruning the leaves tha… text/html 2011-01-17T10:51:44+02:00 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 2010-06-03T13:46:18+02:00 http://treeko.cgenomics.org/doku.php?id=phylome_support&rev=1275565578&do=diff Phylome Support Not all nodes in a species tree are equally well supported. We have designed the phylome support algorithm as an independent tool to measure the robustness of tree nodes independently from the alignment. Instead, large groups of gene trees, usually from the same genome, are used to measure how many times the distribution of nodes can be found. This measure not only provides support for nodes in the tree but also provides the support that alternative topologies would receive for… text/html 2011-01-12T11:52:47+02:00 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 2011-05-16T14:52:17+02:00 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 2010-05-17T16:37:15+02:00 http://treeko.cgenomics.org/doku.php?id=thesis&rev=1274107035&do=diff [ Thesis_2010]