CNCA aligns multiple small, closely related annotated genomes (<50kb, typically virus) using information from protein alignments.
To execute a simple run of CNCA aligner, submit at least two GenBank files and click on RUN.
For more details, see the documentation.

Select File
Default parameters.
Scoring matrix

Scoring matrix for amino acid sequences:

Scoring matrix for nucleotide sequences:

Switch it to '1PAM / κ=2' when aligning closely related DNA sequences.

Gap opening penalty: (1.0 – 5.0)

Offset value: (0.0 – 1.0)

Alignment strategy

Progressive methods

Iterative refinement methods