Split Codons

Separate bases according to codon position

Tool Configuration
Configure the parameters for Split Codons

Paste FASTA coding sequences. Input limit is 500,000,000 characters.

1

Prepare Coding Sequences

Paste your coding DNA sequences in FASTA format. Ensure sequences start at the first codon position for accurate splitting.

2

Execute Codon Splitting

The tool automatically separates each sequence into three new sequences based on codon position (1st, 2nd, and 3rd base of each codon).

3

Review Position Sequences

Three sequences are generated per input: position 1 bases, position 2 bases, and position 3 bases. Partial codons are removed with warnings.

4

Use for Analysis

Download the split sequences for phylogenetic analysis, saturation studies, or GC content analysis by codon position.

Use Cases
Common applications for the Split Codons tool

Codon Position Analysis

Analyze mutation rates or substitution patterns separately for each codon position, as third positions often have different evolutionary constraints.

Phylogenetic Studies

Separate codon positions for phylogenetic analysis, as different positions may evolve at different rates.

Saturation Analysis

Test for substitution saturation by comparing the three codon positions independently.

GC Content Studies

Examine GC content bias at different codon positions to understand compositional heterogeneity.

How Split Codons Works

Example Input Sequence:

ATGATGATG

Codons (groups of 3):

ATG | ATG | ATG

Output Sequences:

Position 1 bases: AAA (first base of each codon)
Position 2 bases: TTT (second base of each codon)
Position 3 bases: GGG (third base of each codon)

Note: If the sequence length is not divisible by 3, the partial codon at the end will be removed and a warning will be issued.

Codon Position Properties

1st Position: Usually determines amino acid class (e.g., hydrophobic vs. polar)
2nd Position: Strongly correlates with chemical properties of amino acids
3rd Position: Often synonymous (wobble position), typically evolves faster due to genetic code redundancy