Visualization software

[arambaut]

Toping listing software for visualizing analyses of viral sequence data including phylogenies, phylogeography and population/epidemiological dynamics.

To add:

• Figtree
• Tracer
• NextStrain
• SpreaD3
• Microreact
• iTol
• R (ggtree package)?
• Aquapony, Densitree?
• other tree software (https://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software)?

[cupton]

Base-By-Base
Visualizes alignments, and differences between sequences.
Shows annotations, and allows comments to be added to sequences.

There are 3 papers that describe BBB over the years:
Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes.

Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments.

Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments.