algorithm

# Differences

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algorithm [2013/06/03 13:00]
mmarcet created
algorithm [2013/06/03 13:15] (current)
mmarcet
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-=== Reconstruction of pruned trees: ===+===== 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 annotations using the extended newick format. Then, for each duplication node, the tree is split in three parts: the main backbone of the tree and the two sister clades that from the duplication node. Trees are reassembled combining the tree backbone with one of the sister clades for each duplication node as seen in the figure. ​ 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 annotations using the extended newick format. Then, for each duplication node, the tree is split in three parts: the main backbone of the tree and the two sister clades that from the duplication node. Trees are reassembled combining the tree backbone with one of the sister clades for each duplication node as seen in the figure. ​
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Note that, in contrast to bootstrap supports that are only informative on the support for a single partition, the phylome support value takes into consideration the specific arrangement between several partitions and it is thus more informative. Additionally it is to be noted that nodes that contain only two leaves will not be considered as they can not have any alternative distribution. Note that, in contrast to bootstrap supports that are only informative on the support for a single partition, the phylome support value takes into consideration the specific arrangement between several partitions and it is thus more informative. Additionally it is to be noted that nodes that contain only two leaves will not be considered as they can not have any alternative distribution.

+----

+  * [[start|Starting page]]
+  * [[documentation|How to run treeKO]]
+  * [[inputfiles|Input Files]]
+  * [[output | Output Files]]
+  * [[configuration_file | Configuration File]]