A congruence index for testing topological similarity between trees
Motivation: Phylogenetic trees are omnipresent in evolutionary biology and the comparison of trees plays a central role there. Tree congruence statistics are based on the null hypothesis that two given trees are not more congruent (topologically similar) than expected by chance. Usually, one searche...
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| Veröffentlicht in: | Bioinformatics 2007-12, Vol.23 (23), p.3119-3124 |
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| creator | de Vienne, Damien M. Giraud, Tatiana Martin, Olivier C. |
| description | Motivation: Phylogenetic trees are omnipresent in evolutionary biology and the comparison of trees plays a central role there. Tree congruence statistics are based on the null hypothesis that two given trees are not more congruent (topologically similar) than expected by chance. Usually, one searches for the most parsimonious evolutionary scenario relating two trees and then one tests the null hypothesis by generating a high number of random trees and comparing these to the one between the observed trees. However, this approach requires a lot of computational work (human and machine) and the results depend on the evolutionary assumptions made. Results: We propose an index, Icong, for testing the topological congruence between trees with any number of leaves, based on maximum agreement subtrees (MAST). This index is straightforward, simple to use, does not rely on parametrizing the likelihood of evolutionary events, and provides an associated confidence level. Availability: A web site has been created that allows rapid and easy online computation of this index and of the associated P-value at http://www.ese.u-psud.fr/bases/upresa/pages/devienne/index.html Contact: damien.de-vienne@u-psud.fr |
| doi_str_mv | 10.1093/bioinformatics/btm500 |
| format | Article |
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Tree congruence statistics are based on the null hypothesis that two given trees are not more congruent (topologically similar) than expected by chance. Usually, one searches for the most parsimonious evolutionary scenario relating two trees and then one tests the null hypothesis by generating a high number of random trees and comparing these to the one between the observed trees. However, this approach requires a lot of computational work (human and machine) and the results depend on the evolutionary assumptions made. Results: We propose an index, Icong, for testing the topological congruence between trees with any number of leaves, based on maximum agreement subtrees (MAST). This index is straightforward, simple to use, does not rely on parametrizing the likelihood of evolutionary events, and provides an associated confidence level. Availability: A web site has been created that allows rapid and easy online computation of this index and of the associated P-value at http://www.ese.u-psud.fr/bases/upresa/pages/devienne/index.html Contact: damien.de-vienne@u-psud.fr</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btm500</identifier><identifier>PMID: 17933852</identifier><identifier>CODEN: BOINFP</identifier><language>eng</language><publisher>Oxford: Oxford University Press</publisher><subject>Algorithms ; Animals ; Biodiversity ; Biological and medical sciences ; Biological Evolution ; Computer Simulation ; Fundamental and applied biological sciences. Psychology ; General aspects ; Genetics, Population ; Host-Parasite Interactions - genetics ; Humans ; Life Sciences ; Mathematics in biology. Statistical analysis. Models. Metrology. 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Tree congruence statistics are based on the null hypothesis that two given trees are not more congruent (topologically similar) than expected by chance. Usually, one searches for the most parsimonious evolutionary scenario relating two trees and then one tests the null hypothesis by generating a high number of random trees and comparing these to the one between the observed trees. However, this approach requires a lot of computational work (human and machine) and the results depend on the evolutionary assumptions made. Results: We propose an index, Icong, for testing the topological congruence between trees with any number of leaves, based on maximum agreement subtrees (MAST). This index is straightforward, simple to use, does not rely on parametrizing the likelihood of evolutionary events, and provides an associated confidence level. Availability: A web site has been created that allows rapid and easy online computation of this index and of the associated P-value at http://www.ese.u-psud.fr/bases/upresa/pages/devienne/index.html Contact: damien.de-vienne@u-psud.fr</description><subject>Algorithms</subject><subject>Animals</subject><subject>Biodiversity</subject><subject>Biological and medical sciences</subject><subject>Biological Evolution</subject><subject>Computer Simulation</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General aspects</subject><subject>Genetics, Population</subject><subject>Host-Parasite Interactions - genetics</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Mathematics in biology. Statistical analysis. Models. Metrology. 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Psychology</topic><topic>General aspects</topic><topic>Genetics, Population</topic><topic>Host-Parasite Interactions - genetics</topic><topic>Humans</topic><topic>Life Sciences</topic><topic>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</topic><topic>Models, Genetic</topic><topic>Phylogeny</topic><topic>Populations and Evolution</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>de Vienne, Damien M.</creatorcontrib><creatorcontrib>Giraud, Tatiana</creatorcontrib><creatorcontrib>Martin, Olivier C.</creatorcontrib><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>ANTE: Abstracts in New Technology & Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Copper Technical Reference Library</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>de Vienne, Damien M.</au><au>Giraud, Tatiana</au><au>Martin, Olivier C.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A congruence index for testing topological similarity between trees</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2007-12-01</date><risdate>2007</risdate><volume>23</volume><issue>23</issue><spage>3119</spage><epage>3124</epage><pages>3119-3124</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><coden>BOINFP</coden><abstract>Motivation: Phylogenetic trees are omnipresent in evolutionary biology and the comparison of trees plays a central role there. Tree congruence statistics are based on the null hypothesis that two given trees are not more congruent (topologically similar) than expected by chance. Usually, one searches for the most parsimonious evolutionary scenario relating two trees and then one tests the null hypothesis by generating a high number of random trees and comparing these to the one between the observed trees. However, this approach requires a lot of computational work (human and machine) and the results depend on the evolutionary assumptions made. Results: We propose an index, Icong, for testing the topological congruence between trees with any number of leaves, based on maximum agreement subtrees (MAST). This index is straightforward, simple to use, does not rely on parametrizing the likelihood of evolutionary events, and provides an associated confidence level. Availability: A web site has been created that allows rapid and easy online computation of this index and of the associated P-value at http://www.ese.u-psud.fr/bases/upresa/pages/devienne/index.html Contact: damien.de-vienne@u-psud.fr</abstract><cop>Oxford</cop><pub>Oxford University Press</pub><pmid>17933852</pmid><doi>10.1093/bioinformatics/btm500</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0002-2685-6478</orcidid><orcidid>https://orcid.org/0000-0001-9532-5251</orcidid><orcidid>https://orcid.org/0000-0002-5295-5963</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Bioinformatics, 2007-12, Vol.23 (23), p.3119-3124 |
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| subjects | Algorithms Animals Biodiversity Biological and medical sciences Biological Evolution Computer Simulation Fundamental and applied biological sciences. Psychology General aspects Genetics, Population Host-Parasite Interactions - genetics Humans Life Sciences Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Genetic Phylogeny Populations and Evolution |
| title | A congruence index for testing topological similarity between trees |
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