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A Practical Guide to Phylogenetics for Nonexperts
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MySSP: non-stationary evolutionary sequence simulation, including indels.

Michael S Rosenberg1

  • 1Center for Evolutionary Functional Genomics and the School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA. msr@asu.edu

Evolutionary Bioinformatics Online
|March 28, 2009
PubMed
Summary
This summary is machine-generated.

MySSP is a new DNA sequence evolution simulation program. It uniquely combines indel simulation, non-stationary patterns, and ancestral sequence output in one package.

Keywords:
DNAIndelsNon-stationaritySequence Simulation

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Evolutionary Genetics

Background:

  • Phylogenetic tree-based DNA sequence evolution simulation is crucial for evolutionary studies.
  • Existing software often lacks comprehensive features for realistic evolutionary modeling.

Purpose of the Study:

  • To introduce MySSP, a novel program for simulating DNA sequence evolution along phylogenetic trees.
  • To address limitations in current software by integrating key simulation features.

Main Methods:

  • MySSP simulates DNA sequence evolution incorporating insertions and deletions (indels).
  • The program allows for flexible, non-stationary evolutionary patterns.
  • MySSP outputs ancestral sequences at various nodes of the phylogenetic tree.

Main Results:

  • MySSP provides a unified platform for complex sequence evolution simulations.
  • The inclusion of indels and non-stationary models enhances simulation realism.
  • Availability of ancestral sequences aids in evolutionary inference.

Conclusions:

  • MySSP offers a unique and powerful tool for researchers studying DNA sequence evolution.
  • Its integrated features facilitate more accurate and comprehensive phylogenetic analyses.