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SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

We present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implement... Full description

Journal Title: Systematic Biology 2016-03-01, Vol.65 (2), p.334-344
Main Author: Mallo, Diego
Other Authors: De Oliveira Martins, Leonardo , Posada, David
Format: Electronic Article Electronic Article
Language: English
Subjects:
Quelle: Alma/SFX Local Collection
Publisher: England: Oxford University Press
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/26526427
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recordid: cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_4748750
title: SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees
format: Article
creator:
  • Mallo, Diego
  • De Oliveira Martins, Leonardo
  • Posada, David
subjects:
  • 0603 Evolutionary Biology
  • 0604 Genetics
  • Classification
  • Classification - methods
  • Computer Simulation
  • Evolution
  • Evolutionary Biology
  • Extinct species
  • Gene conversion
  • gene duplication
  • gene duplication and loss
  • gene family evolution
  • Genes
  • Genes - genetics
  • Genetic heterogeneity
  • Genetic Loci
  • Genetic Loci - genetics
  • Genetic Speciation
  • Genetic variation
  • Genomes
  • horizontal gene transfer
  • incomplete lineage sorting
  • locus tree
  • loss
  • Mathematical models
  • Phylogenetics
  • Phylogeny
  • Population size
  • Reproducibility of Results
  • Simulation
  • Simulations
  • Software
  • Software - standards
  • Software for Systematics
  • SOFTWARE FOR SYSTEMATICS AND EVOLUTION
  • Software packages
  • Speciation
  • species tree
ispartof: Systematic Biology, 2016-03-01, Vol.65 (2), p.334-344
description: We present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 1063-5157
fulltext: fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


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descriptionWe present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases.
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subject0603 Evolutionary Biology ; 0604 Genetics ; Classification ; Classification - methods ; Computer Simulation ; Evolution ; Evolutionary Biology ; Extinct species ; Gene conversion ; gene duplication ; gene duplication and loss ; gene family evolution ; Genes ; Genes - genetics ; Genetic heterogeneity ; Genetic Loci ; Genetic Loci - genetics ; Genetic Speciation ; Genetic variation ; Genomes ; horizontal gene transfer ; incomplete lineage sorting ; locus tree ; loss ; Mathematical models ; Phylogenetics ; Phylogeny ; Population size ; Reproducibility of Results ; Simulation ; Simulations ; Software ; Software - standards ; Software for Systematics ; SOFTWARE FOR SYSTEMATICS AND EVOLUTION ; Software packages ; Speciation ; species tree
ispartofSystematic Biology, 2016-03-01, Vol.65 (2), p.334-344
rights
0Copyright © 2016 Society of Systematic Biologists
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descriptionWe present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases.
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00603 Evolutionary Biology
10604 Genetics
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5Evolution
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7Extinct species
8Gene conversion
9gene duplication
10gene duplication and loss
11gene family evolution
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14Genetic heterogeneity
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17Genetic Speciation
18Genetic variation
19Genomes
20horizontal gene transfer
21incomplete lineage sorting
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23loss
24Mathematical models
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27Population size
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abstractWe present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases.
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