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Phylogenomics with paralogs.(BIOPHYSICS AND COMPUTATIONAL BIOLOGY)(Report)

Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is not necessary. Building upon recen... Full description

Journal Title: Proceedings of the National Academy of Sciences of the United States Feb 17, 2015, Vol.112(7), p.2058
Main Author: Hellmuth, Marc
Other Authors: Wieseke, Nicolas , Lechner, Marcus , Lenhof, Hans-Peter , Middendorf, Martin , Stadler, Peter F.
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: ISSN: 0027-8424
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recordid: gale_ofa433686621
title: Phylogenomics with paralogs.(BIOPHYSICS AND COMPUTATIONAL BIOLOGY)(Report)
format: Article
creator:
  • Hellmuth, Marc
  • Wieseke, Nicolas
  • Lechner, Marcus
  • Lenhof, Hans-Peter
  • Middendorf, Martin
  • Stadler, Peter F.
subjects:
  • Phylogeny – Methods
  • Genomics – Methods
ispartof: Proceedings of the National Academy of Sciences of the United States, Feb 17, 2015, Vol.112(7), p.2058
description: Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is not necessary. Building upon recent advances in mathematical phylogenetics, we demonstrate that gene duplications convey meaningful phylogenetic information and allow the inference of plausible phylogenetic trees, provided orthologs and paralogs can be distinguished with a degree of certainty. Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the noise to find correct event-annotated gene trees. The information of gene trees can then directly be translated into constraints on the species trees. Although the resolution is very poor for individual gene families, we show that genomewide data sets are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal gene transfer. orthology | paralogy | gene tree | species tree | cograph
language: eng
source:
identifier: ISSN: 0027-8424
fulltext: fulltext
issn:
  • 0027-8424
  • 00278424
url: Link


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titlePhylogenomics with paralogs.(BIOPHYSICS AND COMPUTATIONAL BIOLOGY)(Report)
creatorHellmuth, Marc ; Wieseke, Nicolas ; Lechner, Marcus ; Lenhof, Hans-Peter ; Middendorf, Martin ; Stadler, Peter F.
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identifierISSN: 0027-8424
subjectPhylogeny – Methods ; Genomics – Methods
descriptionPhylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is not necessary. Building upon recent advances in mathematical phylogenetics, we demonstrate that gene duplications convey meaningful phylogenetic information and allow the inference of plausible phylogenetic trees, provided orthologs and paralogs can be distinguished with a degree of certainty. Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the noise to find correct event-annotated gene trees. The information of gene trees can then directly be translated into constraints on the species trees. Although the resolution is very poor for individual gene families, we show that genomewide data sets are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal gene transfer. orthology | paralogy | gene tree | species tree | cograph
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titlePhylogenomics with paralogs.(BIOPHYSICS AND COMPUTATIONAL BIOLOGY)(Report)
descriptionPhylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is not necessary. Building upon recent advances in mathematical phylogenetics, we demonstrate that gene duplications convey meaningful phylogenetic information and allow the inference of plausible phylogenetic trees, provided orthologs and paralogs can be distinguished with a degree of certainty. Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the noise to find correct event-annotated gene trees. The information of gene trees can then directly be translated into constraints on the species trees. Although the resolution is very poor for individual gene families, we show that genomewide data sets are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal gene transfer. orthology | paralogy | gene tree | species tree | cograph
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titlePhylogenomics with paralogs.(BIOPHYSICS AND COMPUTATIONAL BIOLOGY)(Report)
authorHellmuth, Marc ; Wieseke, Nicolas ; Lechner, Marcus ; Lenhof, Hans-Peter ; Middendorf, Martin ; Stadler, Peter F.
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abstractPhylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is not necessary. Building upon recent advances in mathematical phylogenetics, we demonstrate that gene duplications convey meaningful phylogenetic information and allow the inference of plausible phylogenetic trees, provided orthologs and paralogs can be distinguished with a degree of certainty. Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the noise to find correct event-annotated gene trees. The information of gene trees can then directly be translated into constraints on the species trees. Although the resolution is very poor for individual gene families, we show that genomewide data sets are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal gene transfer. orthology | paralogy | gene tree | species tree | cograph
pubNational Academy of Sciences
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pages2058-2063
doi10.1073/pnas.1412770112
eissn10916490
date2015-02-17