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Concatenator, a user-friendly program to concatenate DNA sequences, implementing graphical user interfaces for MAFFT

Miguel Vences1, Stefanos Patmanidis2, Vladimir Kharchev1

  • 1Division of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany.

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|January 26, 2023
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Summary

Concatenator is a new GUI program that simplifies multi-gene data analysis for phylogenetic and phylogenomic studies. It efficiently combines, aligns, and explores DNA sequence data in various formats.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic and phylogenomic analyses depend on multi-gene datasets presented in diverse formats.
  • Existing tools often lack user-friendliness for managing complex multi-gene workflows, including combining, concatenating, separating, aligning, and exploring data.

Purpose of the Study:

  • To introduce Concatenator, a graphical user interface (GUI)-driven program designed to streamline the processing of multi-gene DNA sequence data for phylogenetic analyses.
  • To provide a user-friendly solution for combining, concatenating, separating, aligning, and exploring multi-gene datasets.

Main Methods:

  • Concatenator accepts single- and multi-marker DNA sequences in Fasta, Phylip, and Nexus formats.
  • The program outputs concatenated sequences in Fasta, Nexus, or Phylip formats, with options for alignment using MAFFT and exploratory tree generation using FastTree.
  • It is implemented in Python with C extensions and supports phylogenomic datasets up to 30,000 markers.

Main Results:

  • Concatenator offers a user-friendly GUI for efficient multi-gene data handling.
  • The software supports multiple input and output formats, facilitating integration with downstream analyses like model selection in IQ-TREE.
  • It can process large phylogenomic datasets, demonstrating scalability.

Conclusions:

  • Concatenator simplifies complex multi-gene data workflows in phylogenetics and phylogenomics.
  • The program's flexibility and ease of use make it a valuable tool for researchers.
  • Concatenator is readily available for MS Windows and Mac OS, with its source code open-sourced on GitHub.