Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees

Diego Mallo, Leonardo de Oliveira Martins, David Posada
doi: https://doi.org/10.1101/021709
Diego Mallo
Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, 36310, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Leonardo de Oliveira Martins
Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, 36310, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David Posada
Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, 36310, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

We present here a fast and flexible software –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 the 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, pre-compiled executables, a detailed manual and example cases.

Footnotes

  • ↵1 E-mails: dmallo{at}uvigo.es

  • ↵2 leomrtns{at}uvigo.es

  • ↵3 dposada{at}uvigo.es

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted June 30, 2015.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees
Diego Mallo, Leonardo de Oliveira Martins, David Posada
bioRxiv 021709; doi: https://doi.org/10.1101/021709
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees
Diego Mallo, Leonardo de Oliveira Martins, David Posada
bioRxiv 021709; doi: https://doi.org/10.1101/021709

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Evolutionary Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (2517)
  • Biochemistry (4964)
  • Bioengineering (3469)
  • Bioinformatics (15181)
  • Biophysics (6885)
  • Cancer Biology (5380)
  • Cell Biology (7711)
  • Clinical Trials (138)
  • Developmental Biology (4518)
  • Ecology (7135)
  • Epidemiology (2059)
  • Evolutionary Biology (10210)
  • Genetics (7497)
  • Genomics (9767)
  • Immunology (4822)
  • Microbiology (13179)
  • Molecular Biology (5129)
  • Neuroscience (29367)
  • Paleontology (203)
  • Pathology (835)
  • Pharmacology and Toxicology (1460)
  • Physiology (2129)
  • Plant Biology (4734)
  • Scientific Communication and Education (1008)
  • Synthetic Biology (1337)
  • Systems Biology (4002)
  • Zoology (768)