Supplemental

Note

These tools are optional and not needed to run any Basestack feature They are not bundled within Basestack (supplemental to bioinformatic/genomics analysis) and must be downloaded separately. They are (mainly) discussed in the bioinformatics modules of the workshop provided with Basestack

• BEAST v1.10.4:

  • https://beast.community/

  • Available in all 3 OS types

• MEGA X

  • https://www.megasoftware.net/

  • Available in all 3 OS types

• AliView v1.26:

  • https://ormbunkar.se/aliview/downloads/linux/linux-version-1.26/

  • Available in all 3 OS types

• MAFFT v7

• https://mafft.cbrc.jp/alignment/software/

• Available in all 3 OS types

• BEAGLE v3.1.2

build from source (instructions)

• https://github.com/beagle-dev/beagle-lib/

• Available in all 3 OS Types

• TempEst v1.5.3

  • http://tree.bio.ed.ac.uk/software/tempest/

  • Available in all 3 OS Types

• Tracer v1.7.1

  • https://github.com/beast-dev/tracer/releases/tag/v1.7.1

  • Available in all 3 OS Types

• 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/

• 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

• FastTree v2.1.11 (double precision variant)

  • http://www.microbesonline.org/fasttree/

  • Available in all 3 OS Types (Less user-friendly)

• Python3

  • https://www.python.org/downloads/

  • Available in all 3 OS Types

• biopython

  • https://biopython.org/wiki/Download

  • Install after installing/updating Python