aliViz Help
Choose File Load an Alignment with Ref as first seq and SubType as second seq.
Sort Sort sequences by name (REF and SUBTYPE remain first)
Group Group sequences using field in Seq names
Add Founder Set a Founder sequence as consensus of a group
Infer Infer a phylogeny using FastTree of Neighbor Joining
Reroot Reroot tree on subtype sequence
Ladderize Ladderize tree and reorder sequences
Histogram Show histogram of root-to-leaf distances
Cluster Show 2D projection and clustering of pairwise leaf distances
fasta Download current view (NT or AA) as FASTA
tree Export current tree as Newick format
Clear Alignment Remove all sequences
Clear Tree Remove current tree
View Mode Switch between Nucleotide (NT) and Amino Acid (AA) view
Highlighter Highlight differences with respect to Reference, SubType, or Founder
Load Epitopes Load epitope descriptions from CSV file
Select Epitope Select an epitope to restrict display
Show Logo Generate sequence logo for selected epitope
IUPAC Full IUPAC ambiguity codes supported in Nucleotide view