Practical sessions in these modules will involve the software packages listed below.
Phylogenetic Inference:

Virulign (https://github.com/rega-cev/virulign)
Jalview (http://www.jalview.org/Download)
AliView (http://ormbunkar.se/aliview/)
IQ-Tree v1.6.5 (http://www.iqtree.org/#download)
Alistat (https://github.com/thomaskf/AliStat/)
MEGA X (http://www.megasoftware.net/)
FigTree v1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/)


Evolutionary Hypothesis Testing:
BEAST1 v1.10.1 (https://github.com/beast-dev/beast-mcmc/releases)
BEAGLE v3.1.0 (https://github.com/beagle-dev/beagle-lib/releases)
Consel (https://github.com/shimo-lab/consel & http://stat.sys.i.kyoto-u.ac.jp/prog/consel/)
IQ-Tree v1.6.5 (http://www.iqtree.org/#download)
MrBayes v3.2.6 (http://mrbayes.sourceforge.net/download.php)
TREE-PUZZLE 5.3.rc16 (http://www.tree-puzzle.de/#download)
SpreaD3 v0.9.7.1 (https://rega.kuleuven.be/cev/ecv/software/SpreaD3)
FigTree v1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/)
Tracer v1.7.1 (https://github.com/beast-dev/tracer/releases/)
TempEst v1.5.1 (http://tree.bio.ed.ac.uk/software/tempest/)



Next Generation Sequencing:
Uses a VirtualBox image that is prepared by members of the module; hence VirtualBox will be installed on the computers for the NGS module.
Included packages: UGENE, including fastqc, CASAVA, cutadapt, bowtie, BWA, SAMtools, SPAdes, the Tuxedo pipeline, Diamond, Kraken/Clark/WEVOTE metagenomics and MEGAN.
The VirtualBox file is typically around 20 Gb in size, with the imported virtual machine disk taking about 50 to 60 Gb in disk space.
Additional information:
– GUI applications Bandage, Tablet, KNIME (with the SeqAn plugin), and UGENE are installed to the “~/Apps” folder. They can also be run from the Desktop.
– The other tools can be run in the Terminal. They are available in “/usr/bin” and added to the PATH, so just run one of the commands:

  • velvetg, velveth, velvetoptimiser
  • spades
  • blastn, blastp, etc.

Genome Detective (www.genomedetective.com/app/typingtool/virus)

Large Phylogenies:
Fasttree v2.1.10 (http://www.microbesonline.org/fasttree/#Install)
IQ-Tree v1.6.5 (http://www.iqtree.org/#download)
PhyloPart v2.1 (https://sourceforge.net/projects/phylopart/files/)
PhyloType v7 (http://web-mab.lirmm.fr/phylotype/)
RAxML v8.2.12 (https://github.com/stamatak/standard-RAxML/releases)

Transmission clusters:
BEAST2 v2.5.0 (https://www.beast2.org/)
Clusterpicker v1.2.3 (http://hiv.bio.ed.ac.uk/software.html)
PHYML v3.0 (http://www.atgc-montpellier.fr/phyml/binaries.php)
PAUP 4.0a161 – (http://phylosolutions.com/paup-test/)
Sea view v4.7 (http://doua.prabi.fr/software/seaview)
ClustalW v2.1 (http://www.clustal.org/clustal2/#Download)

Molecular Adaption:
HYPHY v2.3.13 (https://github.com/veg/hyphy/releases)

Recombination & Networks:
RDP3 v4.95 (http://web.cbio.uct.ac.za/~darren/rdp.html)
Simplot v3.5.1 (http://sray.med.som.jhmi.edu/SCRoftware/simplot/)
SplitsTree v4 (http://www.splitstree.org/)

Visualization:
FigTree v1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/)
R v3.5.0 (https://cran.r-project.org/bin/windows/base/)
SpreaD3 RC v0.9.7.1 (https://rega.kuleuven.be/cev/ecv/software/SpreaD3)
RStudio v1.1.453 (https://www.rstudio.com/products/rstudio/download/)

Virus Analysis Tools:
Genome Detective (www.genomedetective.com/app/typingtool/virus)