FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2102020547> ?p ?o ?g. }

• W2102020547 abstract "Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost.We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning much of the tree of life, and knowledge of the complete complement of genes in a species' genome. The algorithm, called GIGA, constructs trees agglomeratively from a distance matrix representation of sequences, using simple rules to incorporate this genomic age information. GIGA makes use of a novel conceptualization of gene trees as being composed of orthologous subtrees (containing only speciation events), which are joined by other evolutionary events such as gene duplication or horizontal gene transfer. An important innovation in GIGA is that, at every step in the agglomeration process, the tree is interpreted/reinterpreted in terms of the evolutionary events that created it. Remarkably, GIGA performs well even when using a very simple distance metric (pairwise sequence differences) and no distance averaging over clades during the tree construction process.GIGA is efficient, allowing phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is exceptionally robust to adding more gene sequences, opening up the possibility of creating stable identifiers for referring to not only extant genes, but also their common ancestors. We compared trees produced by GIGA to those in the TreeFam database, and they were very similar in general, with most differences likely due to poor alignment quality. However, some remaining differences are algorithmic, and can be explained by the fact that GIGA tends to put a larger emphasis on minimizing gene duplication and deletion events." @default.
• W2102020547 created "2016-06-24" @default.
• W2102020547 creator A5016853551 @default.
• W2102020547 date "2010-06-09" @default.
• W2102020547 modified "2023-10-08" @default.
• W2102020547 title "GIGA: a simple, efficient algorithm for gene tree inference in the genomic age" @default.
• W2102020547 cites W1799812931 @default.
• W2102020547 cites W1800445109 @default.
• W2102020547 cites W1988471037 @default.
• W2102020547 cites W1990777085 @default.
• W2102020547 cites W2003001917 @default.
• W2102020547 cites W2009234149 @default.
• W2102020547 cites W2017051353 @default.
• W2102020547 cites W2024811317 @default.
• W2102020547 cites W2029833898 @default.
• W2102020547 cites W2060425093 @default.
• W2102020547 cites W2061646232 @default.
• W2102020547 cites W2065375138 @default.
• W2102020547 cites W2074974832 @default.
• W2102020547 cites W2080429646 @default.
• W2102020547 cites W2081933515 @default.
• W2102020547 cites W2097059553 @default.
• W2102020547 cites W2100352148 @default.
• W2102020547 cites W2103546861 @default.
• W2102020547 cites W2109432203 @default.
• W2102020547 cites W2110335151 @default.
• W2102020547 cites W2111229238 @default.
• W2102020547 cites W2113234327 @default.
• W2102020547 cites W2113721899 @default.
• W2102020547 cites W2114250447 @default.
• W2102020547 cites W2128252278 @default.
• W2102020547 cites W2129561668 @default.
• W2102020547 cites W2132023322 @default.
• W2102020547 cites W2141913814 @default.
• W2102020547 cites W2155606054 @default.
• W2102020547 cites W2165140440 @default.
• W2102020547 cites W2276605232 @default.
• W2102020547 cites W3012079654 @default.
• W2102020547 cites W4238681835 @default.
• W2102020547 cites W4240620204 @default.
• W2102020547 cites W4252706339 @default.
• W2102020547 doi "https://doi.org/10.1186/1471-2105-11-312" @default.
• W2102020547 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2905364" @default.
• W2102020547 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/20534164" @default.
• W2102020547 hasPublicationYear "2010" @default.
• W2102020547 type Work @default.
• W2102020547 sameAs 2102020547 @default.
• W2102020547 citedByCount "38" @default.
• W2102020547 countsByYear W21020205472012 @default.
• W2102020547 countsByYear W21020205472013 @default.
• W2102020547 countsByYear W21020205472014 @default.
• W2102020547 countsByYear W21020205472015 @default.
• W2102020547 countsByYear W21020205472016 @default.
• W2102020547 countsByYear W21020205472017 @default.
• W2102020547 countsByYear W21020205472018 @default.
• W2102020547 countsByYear W21020205472019 @default.
• W2102020547 countsByYear W21020205472020 @default.
• W2102020547 countsByYear W21020205472021 @default.
• W2102020547 crossrefType "journal-article" @default.
• W2102020547 hasAuthorship W2102020547A5016853551 @default.
• W2102020547 hasBestOaLocation W21020205471 @default.
• W2102020547 hasConcept C104317684 @default.
• W2102020547 hasConcept C113174947 @default.
• W2102020547 hasConcept C11413529 @default.
• W2102020547 hasConcept C134306372 @default.
• W2102020547 hasConcept C141231307 @default.
• W2102020547 hasConcept C154945302 @default.
• W2102020547 hasConcept C184898388 @default.
• W2102020547 hasConcept C193252679 @default.
• W2102020547 hasConcept C26619641 @default.
• W2102020547 hasConcept C33923547 @default.
• W2102020547 hasConcept C41008148 @default.
• W2102020547 hasConcept C53208351 @default.
• W2102020547 hasConcept C54355233 @default.
• W2102020547 hasConcept C70721500 @default.
• W2102020547 hasConcept C86803240 @default.
• W2102020547 hasConcept C92938381 @default.
• W2102020547 hasConceptScore W2102020547C104317684 @default.
• W2102020547 hasConceptScore W2102020547C113174947 @default.
• W2102020547 hasConceptScore W2102020547C11413529 @default.
• W2102020547 hasConceptScore W2102020547C134306372 @default.
• W2102020547 hasConceptScore W2102020547C141231307 @default.
• W2102020547 hasConceptScore W2102020547C154945302 @default.
• W2102020547 hasConceptScore W2102020547C184898388 @default.
• W2102020547 hasConceptScore W2102020547C193252679 @default.
• W2102020547 hasConceptScore W2102020547C26619641 @default.
• W2102020547 hasConceptScore W2102020547C33923547 @default.
• W2102020547 hasConceptScore W2102020547C41008148 @default.
• W2102020547 hasConceptScore W2102020547C53208351 @default.
• W2102020547 hasConceptScore W2102020547C54355233 @default.
• W2102020547 hasConceptScore W2102020547C70721500 @default.
• W2102020547 hasConceptScore W2102020547C86803240 @default.
• W2102020547 hasConceptScore W2102020547C92938381 @default.
• W2102020547 hasIssue "1" @default.
• W2102020547 hasLocation W21020205471 @default.
• W2102020547 hasLocation W21020205472 @default.
• W2102020547 hasLocation W21020205473 @default.
• W2102020547 hasLocation W21020205474 @default.
• W2102020547 hasLocation W21020205475 @default.
• W2102020547 hasOpenAccess W2102020547 @default.

• next