Alignment¶
Clustal_Omega¶
This module accepts as input a single nucleotide FASTA file, and using the Clustal Omega [2] program, returns as output a single sequence alignment FASTA file. SEDA-CLI operations ([1]; https://hub.docker.com/r/pegi3s/seda/) are performed to reformat files.
Clustal_Omega_codons¶
This module accepts as input a single CDS FASTA file (sequences must not have stop codons), and returns as output a single sequence alignment FASTA file. The provided nucleotide sequences are first translated into amino acid sequences using the EMBOSS transeq feature [3], and an amino acid alignment is obtained using Clustal_Omega [2]. Then, the corresponding nucleotide alignment is obtained using TranslatorX [4]. Therefore, this option is only suitable for FASTA files containing CDS, which is indicated by the “codons” suffix. Sequences must not have stop codons.
Mafft¶
This module accepts as input a single nucleotide FASTA file, and using the MAFFT (https://mafft.cbrc.jp/alignment/software/) program, returns as output a single sequence alignment FASTA file. SEDA-CLI operations ([1]; https://hub.docker.com/r/pegi3s/seda/) are performed in order to remove line breaks from the resulting alignment.
Mafft_codons¶
This module accepts as input a single CDS FASTA file (sequences must not have stop codons), and returns as output a single sequence alignment FASTA file. The provided nucleotide sequences are first translated into amino acid sequences using the EMBOSS transeq feature [3], and an amino acid alignment is obtained using MAFFT (https://mafft.cbrc.jp/alignment/software/). Then, the corresponding nucleotide alignment is obtained using TranslatorX [4]. SEDA-CLI operations ([1]; https://hub.docker.com/r/pegi3s/seda/) are performed in order to remove line breaks from the resulting alignments. This option is only suitable for FASTA files containing CDS, as indicated by the “codons” suffix.
Probcons¶
This module accepts as input a single nucleotide FASTA file, and using the PROBCONS (http://probcons.stanford.edu/manual.pdf) program, returns as output a single sequence alignment FASTA file. SEDA-CLI operations ([1]; https://hub.docker.com/r/pegi3s/seda/) are performed to reformat files.
Probcons_codons¶
This module accepts as input a single CDS FASTA file (sequences must not have stop codons), and returns as output a single sequence alignment FASTA file. The provided nucleotide sequences are first translated into amino acid sequences using the EMBOSS transeq feature [3], and an amino acid alignment is obtained using PROBCONS [http://probcons.stanford.edu/manual.pdf]. Then, the corresponding nucleotide alignment is obtained using TranslatorX [4]. Therefore, this option is only suitable for FASTA files containing CDS, which is indicated by the “codons” suffix. SEDA-CLI operations ([1]; https://hub.docker.com/r/pegi3s/seda/) are performed to reformat files.
Probcons_refinement¶
This module accepts as input a single FASTA file containing aligned sequences, and using the PROBCONS (http://probcons.stanford.edu/manual.pdf) program refinement option, returns a refined FASTA file. The number of iterations (probcons_refin_iterations=) to be executed in the refinement must be specified in the config file.
T-coffee¶
This module accepts as input a single FASTA file, and using the T-coffee [10] program, returns as output a single sequence alignment FASTA file.
T-coffee_codons¶
As indicated by the “codons” suffix, this module accepts as input a single CDS FASTA file (sequences must not have stop codons), and using the T-coffee [10] program, returns as output a single nucleotide alignment FASTA file. The provided nucleotide sequences are first translated into amino acid sequences using the EMBOSS.