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A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences.
Emine Toparslan1, Kemal Karabag2, Ugur Bilge3
1Institute of Natural and Applied Sciences, Akdeniz University, Antalya, Turkey.
Plos One
|December 15, 2020
Summary
This study introduces a new R workflow for phylogenetic analysis using FASTA files. It simplifies extracting haplotypes and visualizing genetic diversity in populations like Bombus terrestris.
Area of Science:
- Molecular Genetics
- Bioinformatics
- Evolutionary Biology
Background:
- Phylogenetic analyses reveal population demography and genetic diversity.
- Molecular genetics generates vast datasets requiring computational analysis.
- Existing software often uses disparate input/output formats, complicating workflows.
Purpose of the Study:
- To present a unified R workflow for phylogenetic analysis.
- To demonstrate haplotype extraction and phylogenetic visualization from FASTA files.
- To simplify complex bioinformatics analyses for R users.
Main Methods:
- Utilized R, an open-source software environment, for data analysis.
- Employed the multiple sequences FASTA format (.fas) as a universal input.
- Applied the workflow to Bombus terrestris mitochondrial cytochrome b gene (cyt b) sequences.
Main Results:
- Successfully extracted haplotypes from the Bombus terrestris dataset.
- Performed phylogenetic analyses and generated visualizations within R.
- Demonstrated the efficiency of a single input format for multiple analyses.
Conclusions:
- The developed R workflow streamlines phylogenetic analysis.
- This approach enhances accessibility for researchers working with molecular data.
- The method is applicable to various species and genetic markers.
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