Translating DNA sequences
To translate dna alignment to amino acid:
segul 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 translate -d loci/ -f fasta --table 2
You can also set the reading frame using the --rf option:
segul translate -d loci/ -f fasta --table 2 --rf 2
To show all the table options, use the --show-tables flag:
segul translate --show-tables
Supported 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 |