CNCA

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

(Get an example of input files)

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(Optional) Run name:

Default parameters.

Scoring matrix

Parameters:

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

Auto (FFT-NS-1, FFT-NS-2, FFT-NS-i or L-INS-i; depends on data size)

Progressive methods

FFT-NS-1 (Very fast; recommended for >2,000 sequences; progressive method)

FFT-NS-2 (Fast; progressive method)

Iterative refinement methods

FFT-NS-i (Slow; iterative refinement method)

E-INS-i (Very slow; recommended for <200 sequences with multiple conserved domains and long gaps; 2 iterative cycles only)

L-INS-i (Very slow; recommended for <200 sequences with one conserved domain and long gaps; 2 iterative cycles only)

G-INS-i (Very slow; recommended for <200 sequences with global homology; 2 iterative cycles only)