Phylogenomics

Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. The abundance of genomic data for an enormous variety of organisms has enabled phylogenomic inference of many groups, and this has motivated the development o...

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Published inMethods in molecular biology (Clifton, N.J.) Vol. 1704; p. 103
Main Authors Patané, José S L, Martins, Jr, Joaquim, Setubal, João C
Format Journal Article
LanguageEnglish
Published United States 01.01.2018
Subjects
Phylogenetic networks
Gene tree
Whole genome
Phylogeny
Species tree
Phylogenomics
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Abstract Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. The abundance of genomic data for an enormous variety of organisms has enabled phylogenomic inference of many groups, and this has motivated the development of many computer programs implementing the associated methods. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.
AbstractList Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. The abundance of genomic data for an enormous variety of organisms has enabled phylogenomic inference of many groups, and this has motivated the development of many computer programs implementing the associated methods. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.
Author Martins, Jr, Joaquim
Patané, José S L
Setubal, João C
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  organization: Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil
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  givenname: Joaquim
  surname: Martins, Jr
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  givenname: João C
  surname: Setubal
  fullname: Setubal, João C
  email: Setubal@iq.usp.br
  organization: Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil. Setubal@iq.usp.br
BackLink https://www.ncbi.nlm.nih.gov/pubmed/29277865$$D View this record in MEDLINE/PubMed
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Keywords Phylogenetic networks
Gene tree
Whole genome
Phylogeny
Species tree
Phylogenomics
Language English
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