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Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector
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Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector

Published on: March 28, 2018

Jackknife and bootstrap tests of the composition vector trees.

Guanghong Zuo1, Zhao Xu, Hongjie Yu

  • 1T-Life Research Center & Department of Physics, Fudan University, Shanghai 200433, China.

Genomics, Proteomics & Bioinformatics
|March 9, 2011
PubMed
Summary
This summary is machine-generated.

Composition vector trees (CVTrees) offer a stable, parameter-free method for inferring prokaryotic phylogenies. Agreement with taxonomy validates these trees, potentially eliminating the need for complex resampling tests.

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A Practical Guide to Phylogenetics for Nonexperts
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A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Phylogenetics

Background:

  • Phylogenetic tree inference is crucial for understanding evolutionary relationships.
  • Traditional methods often rely on sequence alignment and can be computationally intensive.
  • Alignment-free methods offer an alternative for large-scale genomic analysis.

Purpose of the Study:

  • To assess the stability and self-consistency of Composition Vector Trees (CVTrees).
  • To evaluate the utility of CVTrees as an objective method for prokaryotic phylogeny inference.
  • To advocate for the use of taxonomic agreement as a primary validation criterion for CVTrees.

Main Methods:

  • Inference of CVTrees using an alignment-free and parameter-free approach from whole-genome data.
  • Application of bootstrap and jackknife resampling tests adapted for the alignment-free CVTree method.
  • Comparison of inferred CVTree topologies with established prokaryotic taxonomy.

Main Results:

  • CVTrees demonstrate stability and self-consistency under resampling tests.
  • The inferred CVTrees show strong agreement with the established taxonomy.
  • The alignment-free nature of CVTrees simplifies phylogenetic analysis.

Conclusions:

  • CVTrees provide a robust and reliable method for inferring prokaryotic phylogenies.
  • Taxonomic congruence serves as a sufficient criterion for validating CVTree-based phylogenies.
  • The proposed method potentially obviates the need for computationally expensive statistical resampling tests in phylogenetic analysis.