Software
These tools are discussed and used within the Phylogenetics and Bioinformatics modules.
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BEAST v1.10.4:
- https://beast.community/
- Available in all 3 OS types
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MEGA X
- https://www.megasoftware.net/
- Available in all 3 OS types
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AliView v1.26:
- https://ormbunkar.se/aliview/downloads/linux/linux-version-1.26/
- Available in all 3 OS types
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MAFFT v7
- https://mafft.cbrc.jp/alignment/software/
- Available in all 3 OS types
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BEAGLE v3.1.2 build from source (instructions)
- https://github.com/beagle-dev/beagle-lib/
- Available in all 3 OS Types
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TempEst v1.5.3
- http://tree.bio.ed.ac.uk/software/tempest/
- Available in all 3 OS Types
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Tracer v1.7.1
- https://github.com/beast-dev/tracer/releases/tag/v1.7.1
- Available in all 3 OS Types
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FigTree v1.4.4
- http://tree.bio.ed.ac.uk/software/figtree/
- Available in all 3 OS Types
Requires Internet. Also available at https://igv.org/app/
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IQTree v2.1.1
- https://github.com/iqtree/iqtree2/releases
- You will find the executable in the bin sub-folder. Copy all files in bin folder to your system search path such that you can run IQ-TREE by entering iqtree from the Terminal.
- Available in all 3 OS Types
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FastTree v2.1.11 (double precision variant)
- http://www.microbesonline.org/fasttree/
- Available in all 3 OS Types (Less user-friendly)
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Python3
- https://www.python.org/downloads/
- Available in all 3 OS Types
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biopython
- https://biopython.org/wiki/Download
- Install after installing/updating Python
These tools are optional and not needed to run any Basestack feature