Genetic Codes

eskaks supports 20 NCBI translation tables via --genetic-code <N>.

Available tables

eskaks --list-codes

ID	Name	Common use
1	Standard	Default. Most nuclear genes
2	Vertebrate Mitochondrial	Human, mouse, fish mito
3	Yeast Mitochondrial	S. cerevisiae mito
4	Mold/Protozoan/Coelenterate Mito	Also Mycoplasma/Spiroplasma
5	Invertebrate Mitochondrial	Drosophila, C. elegans mito
6	Ciliate Nuclear	Tetrahymena, Paramecium
9	Echinoderm/Flatworm Mito	Sea urchin, planaria mito
10	Euplotid Nuclear	Euplotes
11	Bacterial/Archaeal/Plant Plastid	Prokaryotes, chloroplasts
12	Alternative Yeast Nuclear	Candida
13	Ascidian Mitochondrial	Tunicate mito
14	Alternative Flatworm Mito	Some flatworm mito
16	Chlorophycean Mito	Green algae mito
21	Trematode Mitochondrial	Schistosoma mito
22	Scenedesmus obliquus Mito
23	Thraustochytrium Mito
24	Rhabdopleuridae Mito
25	Candidate Division SR1/Gracilibacteria
26	Pachysolen tannophilus Nuclear
33	Cephalodiscidae Mito (UAA=Tyr)

Usage

# Standard code (default, same as --genetic-code 1)
eskaks fasta genes.fasta

# Vertebrate mitochondrial
eskaks fasta mito_genes.fasta --genetic-code 2

# Bacterial
eskaks fasta prokaryote_genes.fasta --genetic-code 11

How it works

The genetic code affects: - Site classification: Which positions are synonymous vs nonsynonymous - Pathway analysis: Which intermediate codons are stop codons (excluded from pathways) - Degeneracy classification (Li model): 0-fold, 2-fold, 4-fold at each position

Example: AGA encodes Arginine in the standard code but is a stop codon in vertebrate mitochondrial code. This changes both the site counts and the pathway analysis for any codon pair involving AGA.