A new clade starts when the incoming branch length to a node is greater than the threshold. Leaves are grouped by the clade that contains them.
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2D Projection of Pairwise Leaf Distances
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Group Sequences
Color Legend
Groups:
Clusters:
Load 3D structure
Prune by Group
Select groups to remove. Selected groups will be removed from the alignment.
Add Founder Sequence
aliViz Help
(for a full user guide please open: aliViz_userGuide in a new tab)
Choose FileLoad an Alignment with Ref as first seq and SubType as second seq.
SortSort by current grouping, or by name if no grouping (REF and SUBTYPE remain first)
GroupGroup sequences using field in Seq names
PruneRemove sequences from deselected groups
Add FounderSet a Founder sequence as consensus of a group
InferInfer a phylogeny using FastTree of Neighbor Joining
RerootReroot tree on subtype sequence
LadderizeLadderize tree and reorder sequences
HistogramShow histogram of root-to-leaf distances
ClusterShow 2D projection and clustering of pairwise leaf distances
fastaDownload current view (NT or AA) as FASTA
treeExport current tree as Newick format
Clear AlignmentRemove all sequences
Clear TreeRemove current tree
View ModeSwitch between Nucleotide (NT) and Amino Acid (AA) view
HighlighterHighlight differences with respect to Reference, SubType, or Founder
Load EpitopesLoad epitope descriptions from CSV file
Select EpitopeSelect an epitope to restrict display
Show LogoGenerate sequence logo for selected epitope
3D StructureLoad a PDB/CIF file, or enter a 4-character PDB ID and click Fetch to load from RCSB. Chains are added as sequences (xxxx_Chain_y [PDB_y]) and aligned to the reference (AA mode).
View 3DDisplay the loaded PDB structure in a 3D viewer window
IUPACFull IUPAC ambiguity codes supported in Nucleotide view
Group: Not assigned
Cluster: Not assigned
PDB 3D Structure
Epitope residues are colored automatically on intrinsic chains (residue colors, rest gray). Intrinsic = in panel, alignment ≥50%; Extrinsic = in panel, <50%; Superficial = not in panel. Use checkboxes to show/hide chains; set a different style per group.
Intrinsic (≥50%):
Extrinsic (<50%):
Superficial (not in panel):
New epitope (distance-based)
Select one intrinsic and one extrinsic chain. Compute minimum distance from each intrinsic residue to the extrinsic chain; residues below the cutoff form the epitope.