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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Phylogeny-Aware Alignment with PRANK and PAGAN.

Ari Löytynoja1

  • 1Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland. ari.loytynoja@helsinki.fi.

Methods in Molecular Biology (Clifton, N.J.)
|December 8, 2020
PubMed
Summary
This summary is machine-generated.

Accurate sequence alignments are crucial for evolutionary analysis. New software, PRANK and PAGAN, improve sequence alignment by considering evolutionary history and handling insertions/deletions, leading to more reliable phylogenetic inferences.

Keywords:
Character homologyEvolutionary sequence analysisInsertions and deletionsPhylogeny-aware alignment

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Accurate sequence alignments are essential for inferring evolutionary relationships.
  • Traditional alignment methods may not adequately represent evolutionary homology, potentially misleading phylogenetic analyses.
  • Phylogeny-aware alignment algorithms offer improved accuracy by incorporating evolutionary information.

Purpose of the Study:

  • To introduce and discuss the PRANK and PAGAN software packages for phylogeny-aware sequence alignment.
  • To highlight the advantages of these tools in handling insertions and deletions for evolutionary inferences.
  • To provide practical guidance for utilizing PRANK and PAGAN in comparative and phylogenetic studies.

Main Methods:

  • PRANK utilizes a phylogeny-aware algorithm to differentiate and handle insertion/deletion gaps.
  • PAGAN re-implements and enhances the phylogeny-aware approach using sequence graphs for complex gap structures.
  • Both programs infer evolutionary history and provide ancestral sequences as output.

Main Results:

  • PRANK generates accurate alignments for evolutionary inferences by distinguishing gap origins.
  • PAGAN improves upon PRANK by modeling complex gap structures and incorporating uncertainty in ancestral sequence reconstruction.
  • The software packages offer practical solutions for improving the reliability of evolutionary analyses.

Conclusions:

  • Phylogeny-aware alignment, as implemented in PRANK and PAGAN, is critical for accurate evolutionary studies.
  • PAGAN offers advanced capabilities for handling complex evolutionary scenarios and gap uncertainties.
  • These tools are valuable resources for researchers conducting comparative and phylogenetic analyses.