SeqVis Documentation

Click Upload Data on the home page to reach /visjson. Use the Input FASTA file picker to load a .fasta /.phy /.nex file. Files are read in 64 KB streaming chunks so very large genomes (hundreds of MB) load without freezing the browser. A progress bar tracks completion.

• Each >header line starts a new sequence entry.
• Unknown bases (N) and gap characters (- . space) are excluded from frequency counts.
• Frequencies are computed for all positions as well as 1st, 2nd, and 3rd codon positions independently.
• Both UNIX and Windows line endings are normalised automatically.

Use the Input JSON file picker to reload a previously exported SeqVis JSON. The expected schema is an object keyed by sequence name, each entry containing four frequency maps:

{
  "Homo sapiens": {
    "allPositionFreq":   { "A": 0.29, "T": 0.29, "G": 0.21, "C": 0.21 },
    "firstPositionFreq": { "A": 0.30, "T": 0.28, "G": 0.22, "C": 0.20 },
    "secondPositionFreq":{ "A": 0.27, "T": 0.31, "G": 0.20, "C": 0.22 },
    "thirdPositionFreq": { "A": 0.30, "T": 0.28, "G": 0.21, "C": 0.21 }
  },
  ...
}

Click Visualize CSV/TSV on the home page to reach /vistab. Upload any .csv, .tsv, or.tab file with the columns below. This lets you plot published nucleotide composition tables directly without running a sequence alignment.

label,A,T,G,C
Homo sapiens,0.29,0.29,0.21,0.21
Mus musculus,0.28,0.30,0.20,0.22

• First column is the row label (any name).
• Columns A T G C must be decimal proportions summing to ≈ 1.
• Tab-separated files (.tsv / .tab) are auto-detected by extension.

The four Relative Frequency buttons switch the data being plotted without reloading the file. Each codon position can reveal different evolutionary pressures:

Expand the Vertex assignment panel to drag nucleotides between the four tetrahedron corners. This lets you group purines (A+G) or pyrimidines (C+T) onto a single vertex to visualise strand-bias or other compositional patterns.

• Each vertex can hold one or more nucleotide letters (e.g., AG vs CT).
• When a nucleotide is moved, its frequency is added to the destination vertex weight.
• The 3D plot and vertex labels update instantly — no re-upload required.
• Click Reset Tetrahedron to restore the default A/T/G/C layout.

When Auto-scale axes to data maximum is checked, the axis range is set to the highest individual nucleotide frequency present in the dataset (rounded up to the nearest 0.05). This expands the visible region of the tetrahedron so that points fill the space rather than clustering near the centroid.

The current axis max is shown as a badge next to the checkbox when the scale is less than 1. Disable auto-scale to compare multiple datasets on a fixed 0–1 axis.

The Spread slider (0–100%) applies a visual-only radial expansion to separate overlapping dots. It does not alter the underlying frequency data or the exported JSON.

• The tetrahedron inradius bounds the spread so no point can exit the shape.
• Relative distances between points are preserved — nearby sequences stay nearby.
• Spread re-applies automatically when vertex assignment changes.
• A badge on the 3D view indicates when spread is active.

The right panel is a live Three.js canvas. All standard OrbitControls gestures apply:

Three export options are available in the Export section of the left panel: