SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree

John R. Stevens, Todd R. Jones, Michael Lefevre, Balasubramanian Ganesan, Bart C Weimer

Research output: Contribution to journalShort survey

1 Citation (Scopus)

Abstract

Microbial community analysis experiments to assess the effect of a treatment intervention (or environmental change) on the relative abundance levels of multiple related microbial species (or operational taxonomic units) simultaneously using high throughput genomics are becoming increasingly common. Within the framework of the evolutionary phylogeny of all species considered in the experiment, this translates to a statistical need to identify the phylogenetic branches that exhibit a significant consensus response (in terms of operational taxonomic unit abundance) to the intervention. We present the R software package SigTree, a collection of flexible tools that make use of meta-analysis methods and regular expressions to identify and visualize significantly responsive branches in a phylogenetic tree, while appropriately adjusting for multiple comparisons.

Original languageEnglish (US)
Pages (from-to)372-378
Number of pages7
JournalComputational and Structural Biotechnology Journal
Volume15
DOIs
StatePublished - 2017

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Phylogeny
Genomics
Meta-Analysis
Software
Software packages
Experiments
Throughput

Keywords

  • Microbial community analysis
  • Microbial informatics
  • Microbiome
  • Phylogenetic tree

ASJC Scopus subject areas

  • Biotechnology
  • Structural Biology
  • Biophysics
  • Biochemistry
  • Genetics
  • Computer Science Applications

Cite this

SigTree : A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree. / Stevens, John R.; Jones, Todd R.; Lefevre, Michael; Ganesan, Balasubramanian; Weimer, Bart C.

In: Computational and Structural Biotechnology Journal, Vol. 15, 2017, p. 372-378.

Research output: Contribution to journalShort survey

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