Visualization software

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

To add:

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.