Sequence Translation

To translate DNA alignment to amino acid:

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

The app will default to the standard code table (NCBI Table 1). Use the --table option to set the translation table. 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 --reading-frame option:

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

To let SEGUL detect the reading frame of each alignment, use the --auto-read flag instead:

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

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

segul sequence translate --show-tables

Supported translation 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

Sources: NCBI Genetic Code Tables

All options

Option	Description
-d, --dir	Directory with alignments
-i, --input	Alignment files. Allows wildcards
-f, --input-format	Input format: auto (default), fasta, nexus, or phylip
--datatype	Data type: dna (default), aa, or ignore
--table	NCBI translation table. Default: 1
--reading-frame	Reading frame: 1 (default), 2, or 3
--auto-read	Detect the reading frame of each alignment
--show-tables	Print the supported translation tables
-F, --output-format	Output format: nexus (default), phylip, fasta, nexus-int, phylip-int, or fasta-int
-o, --output	Output directory. Default: Sequence-Translate
--force	Overwrite an existing output directory
--log	Log file path. Default: segul.log