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A Practical Guide to Phylogenetics for Nonexperts
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SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees.

Dan F DeBlasio1, Jennifer H Wisecaver2

  • 1Department of Computer Science, University of Arizona , Tucson , AZ , United States.

Peerj
|September 17, 2016
PubMed
Summary

We developed SICLE, a new software tool for phylogenetic analysis. It helps identify and quantify evolutionary relationships, revealing intriguing links between bacteria and archaea in the Salinibacter ruber phylome.

Keywords:
High-throughputNext-generation sequencingPhylogeny

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic analysis is crucial for understanding evolutionary relationships.
  • Automated phylogenetic pipelines generate vast amounts of data that require efficient summarization.
  • Identifying nearest neighbors and support values for nodes in phylogenetic trees is computationally intensive.

Purpose of the Study:

  • To introduce SICLE (Sister Clade Extractor), a novel software tool for high-throughput phylogenetic analysis.
  • To provide an easy-to-use command-line utility for describing nearest neighbors to a node of interest in a phylogenetic tree.
  • To enable rapid identification and quantification of evolutionary relationships meriting further investigation.

Main Methods:

  • SICLE was developed as a command-line utility, embeddable in analysis pipelines or usable as a C++ subroutine.
  • The software was tested on the published phylome of Salinibacter ruber, analyzing 4,589 gene phylogenies.
  • SICLE identifies sister clades and quantifies the support for these relationships.

Main Results:

  • SICLE identified 13 unique sister relationships for Salinibacter ruber across 4,589 gene phylogenies.
  • Salinibacter ruber predominantly grouped with other bacteria, particularly Bacteriodetes.
  • A significant finding was 91 phylogenies showing a sister association between S. ruber and Archaea, suggesting horizontal gene transfer.

Conclusions:

  • SICLE effectively summarizes phylogenetic information from automated pipelines.
  • The tool facilitates the rapid discovery of evolutionarily intriguing relationships, such as potential horizontal gene transfer events.
  • SICLE is a valuable resource for researchers investigating evolutionary history and microbial genomics.