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PUmPER: phylogenies updated perpetually.

Fernando Izquierdo-Carrasco1, John Cazes, Stephen A Smith

  • 1Scientific Computing Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Baden-Württemberg, Germany, Texas Advanced Computing Center, University of Texas, Austin, TX, 78758, USA, University of Michigan, Ann Arbor Department of Ecology and Evolutionary Biology, 48109, MI, USA and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, 76128 Karlsruhe, Baden-Württemberg, Germany.

Bioinformatics (Oxford, England)
|January 31, 2014
PubMed
Summary
This summary is machine-generated.

Maintaining up-to-date phylogenetic trees is challenging due to computational costs. PUmPER automates the perpetual construction and updating of large phylogenetic trees using new sequence data, ensuring accuracy without manual intervention.

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Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Public databases continuously receive new molecular sequence data.
  • Constructing large-scale phylogenetic trees and alignments is computationally intensive and time-consuming.
  • Keeping comprehensive phylogenies updated with the latest sequences presents a significant challenge.

Purpose of the Study:

  • To introduce PUmPER, a novel framework for the perpetual construction of multi-gene alignments and phylogenetic trees.
  • To automate the updating of large phylogenetic trees for specific taxonomic groups using new sequence data.
  • To provide a solution for maintaining accurate and up-to-date phylogenies with minimal human intervention.

Main Methods:

  • PUmPER utilizes PHLAWD for multi-gene alignments and ExaML or RAxML-Light for phylogenetic tree inference.
  • The framework automatically extends alignments and infers updated trees when new sequences become available in GenBank.
  • It leverages previously inferred smaller trees as starting topologies for efficient updates.
  • PUmPER can operate in stand-alone mode or utilize parallel computing clusters for intensive tasks.

Main Results:

  • PUmPER enables the perpetual updating of large phylogenetic trees for specified NCBI taxonomic groups.
  • The framework automates the process of incorporating new sequence data into existing phylogenetic analyses.
  • Phylogenetic trees generated by PUmPER are statistically comparable to those inferred from scratch.

Conclusions:

  • PUmPER offers an automated and efficient solution for maintaining comprehensive and up-to-date phylogenetic trees.
  • The framework significantly reduces the manual effort and computational resources required for phylogenetic analysis.
  • This approach ensures that evolutionary and phylogenetic analyses are based on the most current molecular sequence data available.