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A Practical Guide to Phylogenetics for Nonexperts
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New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics.

Alexander Knyshov1, Eric R L Gordon2, Christiane Weirauch1

  • 1Department of Entomology, University of California, Riverside, Riverside, CA, USA.

Peerj
|April 14, 2021
PubMed
Summary
This summary is machine-generated.

ALiBaSeq software efficiently retrieves targeted sequences from whole genomic sequencing data for phylogenetic analysis. It outperforms existing tools in accuracy and gene recovery across diverse datasets.

Keywords:
AlignmentBLASTHMMEROrthoDBOrthologyPhylogenomicsUCE

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Analyzing whole genomic sequencing (WGS) data for phylogenetic analysis presents challenges, particularly in targeted sequence retrieval.
  • Existing bioinformatics tools often struggle with deep phylogenetic levels and may yield false positives due to amino-acid space searches.
  • Installation difficulties and limited user resources hinder the adoption of current WGS analysis tools.

Purpose of the Study:

  • To introduce a novel program for targeted sequence retrieval from WGS data to facilitate phylogeny generation.
  • To evaluate the performance of the new program against existing bioinformatics tools.
  • To provide a user-friendly and adaptable solution for ortholog retrieval across various WGS data types.

Main Methods:

  • Developed a Python-based program utilizing freely available similarity search tools for homolog detection in assembled WGS data.
  • Compared the program's performance with existing tools using two divergent insect species (>200 My) with annotated genomes.
  • Assessed performance on datasets of highly conserved and variable loci, and diverse WGS assembly types (shotgun, target capture).

Main Results:

  • The developed software successfully retrieves orthologs from diverse WGS assemblies, including unannotated and low-depth data.
  • It demonstrates superior performance by recovering the highest number of genes with maximal coverage and a low false positive rate.
  • ALiBaSeq consistently outperformed other evaluated tools in generating comprehensive and accurate phylogenetic alignments across all tested datasets.

Conclusions:

  • ALiBaSeq offers a robust and flexible solution for targeted sequence retrieval from WGS data, crucial for phylogenetic studies.
  • The software addresses limitations of existing tools, particularly for deep phylogenetic analyses and diverse data types.
  • Freely available with tutorials and a manual, ALiBaSeq enhances the accessibility and accuracy of WGS data analysis for evolutionary research.