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/)
HYPHY v2.3.13 (https://github.com/veg/hyphy/releases)
RDP5.24 (http://web.cbio.uct.ac.za/~darren/rdp.html)
Simplot v3.5.1 (https://sray.med.som.jhmi.edu/SCRoftware/SimPlot/)
SplitsTree v4 (https://software-ab.informatik.uni-tuebingen.de/download/splitstree4/welcome.html)
Evolutionary Hypothesis Testing:
BEAST1 v1.10.4 (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/)