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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Published on: February 3, 2023

NU-IN: Nucleotide evolution and input module for the EvolSimulator genome simulation platform.

Katrina M Dlugosch1, Michael S Barker, Loren H Rieseberg

  • 1Department of Botany, University of British Columbia, Vancouver, BC V6T1Z4, Canada. katrina.dlugosch@gmail.com.

BMC Research Notes
|August 4, 2010
PubMed
Summary
This summary is machine-generated.

The NU-IN software extension enables simulations of nucleotide and amino acid evolution, gene copy number, and gene family dynamics in related genomes. This open-source tool enhances biological realism for genomic data analysis.

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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Published on: May 28, 2021

Area of Science:

  • Genomics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Simulating gene and gene family evolution across genomes is crucial for hypothesis testing.
  • Existing tools like EvolSimulator lack nucleotide evolution and user-defined sequence input, limiting realism.
  • Incorporating synonymous nucleotide evolution and user-specified data enhances comparative genomic studies.

Purpose of the Study:

  • To extend the EvolSimulator platform with enhanced evolutionary simulation capabilities.
  • To enable simulations incorporating synonymous nucleotide evolution and user-defined genomic data.
  • To increase the biological realism and flexibility of genomic evolution simulations.

Main Methods:

  • Developed the NU-IN extension module for EvolSimulator using modified C++ source code.
  • Implemented synonymous and non-synonymous nucleotide evolution.
  • Enabled the use of real or simulated sequence data, gene family specification, and biased gene retention modeling.

Main Results:

  • The NU-IN module fully implements nucleotide evolution (synonymous and non-synonymous).
  • Users can initiate simulations with real or previously simulated sequence data.
  • Demonstrated NU-IN's capability by simulating polyploidy with copy number variation using real genomic data.

Conclusions:

  • NU-IN is an open-source extension for EvolSimulator, available under GNU GPLv3 license.
  • It allows simulation of drift and selection at nucleotide, amino acid, copy number, and gene family levels.
  • Facilitates generation of diverse, biologically realistic simulated genomic datasets for various evolutionary scenarios.