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Updated README
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mdcjansen committed Jul 20, 2023
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3. [sangerseq_viewer](https://github.com/ponnhide/sangerseq_viewer) is utilised to produce a chromatogram for each of the input species found
4. [BLAST](https://doi.org/10.1016/S0022-2836(05)80360-2) is performed on the input fasta sequence against the input reference sequences
5. Multple sequence alignment is performed with [MUSCLE](https://doi.org/10.1101/2021.06.20.449169)
6. DBA initates [Jalview](https://doi.org10.1093/bioinformatics/btp033) for manual review and trimming of alignment data
6. DBA initates [Jalview](https://doi.org/10.1093/bioinformatics/btp033) for manual review and trimming of alignment data
7. [MEGA11](https://doi.org/10.1093/molbev/msab120) is used to perform phylogentic analysis and produce a consensus tree
8. If specified, supplemental data used during analysis is moved to the output folder and the analysis ends.

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## Acknowledgements
DBA uses the following tools in the pipeline:
* [BLAST](https://doi.org/10.1016/S0022-2836(05)80360-2)
* [Jalview](https://doi.org10.1093/bioinformatics/btp033)
* [Jalview](https://doi.org/10.1093/bioinformatics/btp033)
* [MEGA11](https://doi.org/10.1093/molbev/msab120)
* [MUSCLE](https://doi.org/10.1101/2021.06.20.449169)
* [sangerseq_viewer](https://github.com/ponnhide/sangerseq_viewer)
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