Sequence Translation

To translate dna alignment to amino acid:

segul sequence translate -d [path-to-alignment-files] -f [sequence-format-keyword]

By default, the app will use the standard code table (NCBI Table 1). To set the translation table, use the --table option. For example, to translate dna sequences using NCBI Table 2 (vertebrate MtDNA):

segul sequence translate -d loci/ -f fasta --table 2

You can also set the reading frame using the --rf option:

segul sequence translate -d loci/ -f fasta --table 2 --rf 2

To show all the table options, use the --show-tables flag:

segul sequence translate --show-tables

Supported Translation Tables

Sources: NCBI Genetic Code Tables:

Table No	Genetic Code
1	The Standard Code
2	The Vertebrate Mitochondrial Code
3	The Yeast Mitochondrial Code
4	The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
5	The Invertebrate Mitochondrial Code
6	The Ciliate, Dasycladacean and Hexamita Nuclear Code
9	The Echinoderm and Flatworm Mitochondrial Code
10	The Euplotid Nuclear Code
11	The Bacterial, Archaeal and Plant Plastid Code
12	The Alternative Yeast Nuclear Code
13	The Ascidian Mitochondrial Code
14	The Alternative Flatworm Mitochondrial Code
16	Chlorophycean Mitochondrial Code
21	Trematode Mitochondrial Code
22	Scenedesmus obliquus Mitochondrial Code
23	Thraustochytrium Mitochondrial Code
24	Rhabdopleuridae Mitochondrial Code
25	Candidate Division SR1 and Gracilibacteria Code
26	Pachysolen tannophilus Nuclear Code
29	Mesodinium Nuclear Code
30	Peritrich Nuclear Code
33	Cephalodiscidae Mitochondrial UAA-Tyr Code