We are analyzing https://link.springer.com/protocol/10.1007/978-1-61779-582-4_9.

Title:
Inferring Orthology and Paralogy | SpringerLink
Description:
The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree inference and protein function annotation. In this chapter, we provide an overview...
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Keywords {🔍}

google, scholar, doi, url, article, gene, bioinformatics, orthology, biol, pubmed, cas, orthologs, methods, molecular, dessimoz, phylogenetic, tree, res, evolutionary, christophe, trees, jan, database, genomics, mol, acids, analysis, chapter, springer, nucleic, genome, bmc, protocol, adrian, inference, groups, david, sep, issuedd, data, search, altenhoff, biology, genes, anisimova, syst, families, michael, evol, privacy,

Topics {✒️}

springer science+business media gane ka-shu wong approximate likelihood-ratio test hybrid micro-macroevolutionary approach maximum-likelihood phylogenetic estimation month download article/chapter high-throughput ortholog prediction large-scale orthology inference comprehensive multi-species collection gene/species tree reconciliation org/cgi/content/full/21/11/2596 ann-charlotte berglund-sonnhammer marc robinson-rechavi jean-franois dufayard privacy choices/manage cookies mirkin-muchnik-smith conjecture lachlan james coin vera van noort arbeitspapiere der gmd jean-karim hrich ann-charlotte berglund tree-based approaches device instant download homology relations based tree pattern matching pairwise species comparisons gene tree reconstruction jean-philippe doyon orthology analysisusing mcmc altenhoff & christophe dessimoz european economic area review typical applications future methodological developments abel ureta-vidal low genetic variability reduced microevolutionary rate jacob de vlieg theorem-proving procedures modeling cellular machinery i-hisen wu anne-muriel arigon anne-sophie sertier author information authors horizontal gene transfer infer gene duplication genome-scale approaches multi-genome repository benchmarking orthology predictions graph-based approaches conditions privacy policy

Questions {❓}

How confident can we be that orthologs are similar, but paralogs differ?
Is it better to add taxa or characters to a difficult phylogenetic problem?

Schema {🗺️}

ScholarlyArticle:
      headline:Inferring Orthology and Paralogy
      pageEnd:279
      pageStart:259
      image:https://media.springernature.com/w153/springer-static/cover/book/978-1-61779-582-4.jpg
      genre:
         Springer Protocols
      isPartOf:
         name:Evolutionary Genomics
         isbn:
            978-1-61779-582-4
            978-1-61779-581-7
         type:Book
      publisher:
         name:Humana Press
         logo:
            url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
            type:ImageObject
         type:Organization
      author:
            name:Adrian M. Altenhoff
            affiliation:
                  name:ETH Zurich
                  address:
                     name:Department of Computer Science, ETH Zurich, Zurich, Switzerland
                     type:PostalAddress
                  type:Organization
                  name:Swiss Institute of Bioinformatics
                  address:
                     name:Swiss Institute of Bioinformatics, Lausanne, Switzerland
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Christophe Dessimoz
            affiliation:
                  name:ETH Zurich
                  address:
                     name:Department of Computer Science, ETH Zurich, Zurich, Switzerland
                     type:PostalAddress
                  type:Organization
                  name:Swiss Institute of Bioinformatics
                  address:
                     name:Swiss Institute of Bioinformatics, Lausanne, Switzerland
                     type:PostalAddress
                  type:Organization
            email:[email protected]
            type:Person
      keywords:Orthology, Paralogy, Tree reconciliation, Orthology benchmarking
      description:The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree inference and protein function annotation. In this chapter, we provide an overview of the methods used to infer orthology and paralogy. We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation. We discuss conceptual differences among the various orthology inference methods and databases, and examine the difficult issue of verifying and benchmarking orthology predictions. Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments.
      datePublished:2012
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Book:
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      isbn:
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         978-1-61779-581-7
Organization:
      name:Humana Press
      logo:
         url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
         type:ImageObject
      name:ETH Zurich
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      name:Swiss Institute of Bioinformatics
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         name:Swiss Institute of Bioinformatics, Lausanne, Switzerland
         type:PostalAddress
      name:ETH Zurich
      address:
         name:Department of Computer Science, ETH Zurich, Zurich, Switzerland
         type:PostalAddress
      name:Swiss Institute of Bioinformatics
      address:
         name:Swiss Institute of Bioinformatics, Lausanne, Switzerland
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      name:Adrian M. Altenhoff
      affiliation:
            name:ETH Zurich
            address:
               name:Department of Computer Science, ETH Zurich, Zurich, Switzerland
               type:PostalAddress
            type:Organization
            name:Swiss Institute of Bioinformatics
            address:
               name:Swiss Institute of Bioinformatics, Lausanne, Switzerland
               type:PostalAddress
            type:Organization
      name:Christophe Dessimoz
      affiliation:
            name:ETH Zurich
            address:
               name:Department of Computer Science, ETH Zurich, Zurich, Switzerland
               type:PostalAddress
            type:Organization
            name:Swiss Institute of Bioinformatics
            address:
               name:Swiss Institute of Bioinformatics, Lausanne, Switzerland
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Department of Computer Science, ETH Zurich, Zurich, Switzerland
      name:Swiss Institute of Bioinformatics, Lausanne, Switzerland
      name:Department of Computer Science, ETH Zurich, Zurich, Switzerland
      name:Swiss Institute of Bioinformatics, Lausanne, Switzerland
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