treeko.cgenomics.org

treeko [TreeKo]

Comparisons between tree topologies provide important information for many evolutionary studies. TreeKo is a method that allows the comparison of any two tree topologies. Even those with missing leaves and duplications. This is important in genome-wide analysis. Since many trees do not have exact leaf pairings and therefore most tree comparison methods are rendered useless. In order to calculate the distance between two trees that contain duplications, treeKo first prunes the trees. How to run treeKO.

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treeko [TreeKo] | treeko.cgenomics.org Reviews

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Comparisons between tree topologies provide important information for many evolutionary studies. TreeKo is a method that allows the comparison of any two tree topologies. Even those with missing leaves and duplications. This is important in genome-wide analysis. Since many trees do not have exact leaf pairings and therefore most tree comparison methods are rendered useless. In order to calculate the distance between two trees that contain duplications, treeKo first prunes the trees. How to run treeKO.

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treeko [TreeKo] | treeko.cgenomics.org Reviews

https://treeko.cgenomics.org

Comparisons between tree topologies provide important information for many evolutionary studies. TreeKo is a method that allows the comparison of any two tree topologies. Even those with missing leaves and duplications. This is important in genome-wide analysis. Since many trees do not have exact leaf pairings and therefore most tree comparison methods are rendered useless. In order to calculate the distance between two trees that contain duplications, treeKo first prunes the trees. How to run treeKO.

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treeko.cgenomics.org

1

inputfiles [TreeKo]

http://treeko.cgenomics.org/inputfiles

Input files accepted by treeKO. TreeKO's configuration file. Input files accepted by treeKO. In order to use it, each internal node in the tree should be labeled with a tag like & NHX:evoltype= S in the case of a speciation node or like & NHX:evoltype= D in the case of a duplication node. See the example below:. Additionally you can mark horizontal gene transfer events on your tree. In this case the node will be annotated as & NHX:HGT=True. Instead of a second tree, a list of trees can also be provided&#...

2

about [TreeKo]

http://treeko.cgenomics.org/about

TreeKO is developed at the Gabaldón's lab ( http:/ gabaldonlab.crg.es. At the Centre for Genomic Regulation (Barcelona, Spain). Mmarcet [ at ] crg.es. Tgabaldon [ at ] crg.es. For any question regarding the use of treeKO or to report bugs in the program, you can join our google group:. Http:/ groups.google.com/group/treeko-support. If you use treeKO please cite:. Jaime Huerta-Cepas, Joaquín Dopazo and Toni Gabaldón. ETE: a python Environment for Tree Exploration. BMC Bioinformatics 2010, 11:24.

3

algorithm [TreeKo]

http://treeko.cgenomics.org/algorithm

Reconstruction of pruned trees:. 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. Reconstruction of pruned trees:. Then treeKO will first split the tree into pruned tree dividing it by each nod...

4

downloads [TreeKo]

http://treeko.cgenomics.org/downloads

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. How to run treeKO. Downloads.txt Last modified: 2013/06/03 13:18 by mmarcet. Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution 3.0 Unported.

5

configuration_file [TreeKo]

http://treeko.cgenomics.org/configuration_file

Options regarding tree rooting:. Options regarding treeKO thresholds:. 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 #. Orto mode tab s/r/m. Orthology and paralogy nodes will be predicted using the species overlap algorithm. Tree comparison, Phyl...

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big.crg.cat

Comparative Genomics | Bioinformatics and Genomics @ CRG

http://big.crg.cat/comparative_genomics

Research in our lab. Comparative genomics of fungal pathogens. Phylogenomics and genome evolution through large-scale phylogenetics. Mitochondria and peroxisomes and their role in disease. Evolution of cell death pathways. Evolution of the eukaryotic cell: mitochondria and peroxisomes. Environment for Tree Exploration (ETE). Comparative transcriptomics of early dipteran development. Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates. Mol Biol. Evol. Nat Rev. Genet.

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treeko.cgenomics.org

treeko [TreeKo]

Comparisons between tree topologies provide important information for many evolutionary studies. TreeKo is a method that allows the comparison of any two tree topologies. Even those with missing leaves and duplications. This is important in genome-wide analysis. Since many trees do not have exact leaf pairings and therefore most tree comparison methods are rendered useless. In order to calculate the distance between two trees that contain duplications, treeKo first prunes the trees. How to run treeKO.

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Window.devicePixelRatio*screen.width 'x' window.devicePixelRatio*screen.height) :(screen.width 'x' screen.height) " class="mi". Window.devicePixelRatio*screen.width 'x' window.devicePixelRatio*screen.height) :(screen.width 'x' screen.height) ". Join DeviantArt for FREE. Forgot Password or Username? Treek is all you need! Deviant for 7 Years. This deviant's full pageview. November 30, 1992. Last Visit: 34 weeks ago. Treek is all you need! This is the place where you can personalize your profile! I'm surpr...

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