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.

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.

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.