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A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
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Published on: July 11, 2025

Mlcoalsim: multilocus coalescent simulations.

Sebastian E Ramos-Onsins1, Thomas Mitchell-Olds

  • 1Max-Planck Institute for Chemical Ecology, Hans-Knöll Str. 8, D-07745 Jena, Germany. sramosonsins@ub.edu

Evolutionary Bioinformatics Online
|May 12, 2009
PubMed
Summary
This summary is machine-generated.

mlcoalsim is a new software tool that enhances coalescent simulations for population genetics and molecular evolution research. It improves methods, models, and analyses, including multilocus data, to test evolutionary hypotheses with DNA variation data.

Keywords:
Coalescent simulationsMultilocus analysesNeutrality testsPopulation GeneticsRejection algorithm

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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Area of Science:

  • Population Genetics
  • Molecular Evolution
  • Computational Biology

Background:

  • Coalescent theory is crucial for understanding DNA variation patterns.
  • Monte Carlo simulations generate empirical distributions for hypothesis testing.
  • Existing tools have limitations in modeling complex evolutionary scenarios.

Purpose of the Study:

  • To introduce mlcoalsim, an enhanced software application for coalescent simulations.
  • To improve methodologies, evolutionary models, and analytical capabilities in population genetics.
  • To facilitate the analysis of DNA variation data, particularly multilocus data.

Main Methods:

  • Utilizes coalescent Monte Carlo simulations.
  • Incorporates advanced features for mutation and recombination uncertainty and conditioning.
  • Includes models for positive selection, finite sites, and rate heterogeneity.
  • Analyzes multilocus data in linked and independent regions.

Main Results:

  • mlcoalsim provides improved methodology for evolutionary analyses.
  • The software supports a wider range of evolutionary models, including selection and heterogeneity.
  • It enables calculation of population genetics statistics and P-values for observed data.
  • Facilitates comprehensive analysis of multilocus DNA variation.

Conclusions:

  • mlcoalsim is a valuable integrated software application for molecular evolution researchers.
  • It offers enhanced capabilities for testing evolutionary hypotheses using empirical data.
  • The tool supports advanced analyses of DNA variation, especially multilocus data.