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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Published on: August 14, 2018

GenNon-h: generating multiple sequence alignments on nonhomogeneous phylogenetic trees.

Anna M Kedzierska1, Marta Casanellas

  • 1Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain.

BMC Bioinformatics
|August 30, 2012
PubMed
Summary

This study introduces GenNon-h, a novel software package for generating DNA multiple sequence alignments (MSAs) directly from discrete-time Markov processes on phylogenetic trees. It enables the simulation of nonhomogeneous data, advancing phylogenetic analysis.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Phylogenetics

Background:

  • Existing software for DNA multiple sequence alignment (MSA) generation is limited to time-reversible models and continuous-time Markov processes.
  • There is a lack of methods to directly simulate DNA MSAs from transition matrices.
  • Current tools are not optimized for generating nonhomogeneous data with lineage-specific substitution rates.

Purpose of the Study:

  • To develop the first software package for generating DNA MSAs under discrete-time Markov processes on phylogenetic trees.
  • To enable direct simulation of MSAs from probability substitution matrices.
  • To provide a tool for generating nonhomogeneous phylogenetic data.

Main Methods:

  • Developed a novel algorithm implemented in the GenNon-h package.
  • Utilizes discrete-time Markov processes on phylogenetic trees.
  • Accepts input models and phylogenetic trees in Newick format with branch lengths representing expected substitutions per site.

Main Results:

  • Successfully created the GenNon-h package, the first of its kind for generating DNA MSAs from discrete-time Markov processes.
  • The software generates DNA alignments of desired length based on user-defined models and trees.
  • GenNon-h is publicly available for download.

Conclusions:

  • GenNon-h is an efficient tool for generating DNA MSAs on specified phylogenetic trees.
  • The software facilitates the creation of nonstationary or nonhomogeneous phylogenetic data.
  • This data is valuable for testing complex biological hypotheses and assessing the robustness of reconstruction algorithms.