v3.5.0

Added the ComputeMSA module to compute MSAs from allele calling results or from a folder containing FASTA files. The ComputeMSA module includes the following functionalities:

• Compute loci, sample and complete MSAs based on the allelic profiles determined by chewBBACA (e.g. at the wg/cgMLST level). Gap sequences (the character used to represent gaps is -) are added whenever a locus was not identified in a sample (e.g. when working at the wgMLST level).
• Compute a MSA for each FASTA file in a folder (just a way to run MAFFT to compute MSAs).
• MSAs can be computed both at the protein and DNA level (i.e. by converting protein MSAs back to DNA).
• The --output-variable option identifies the variable positions (SNVs) and creates MSAs only for those positions. When determining variable positions, positions with gaps or ambiguous bases can be excluded (--gaps exclude and --ambiguous exclude) or included (--gaps ignore and --ambiguous ignore) in the MSA if the sequences have other variable non-gap and non-ambiguous nucleotides or amino acids.
• The SchemaEvaluator and AlleleCallEvaluator modules use the ComputeMSA module to compute the loci MSAs (SchemaEvaluator) and the complete MSA used by FastTree to compute a tree (AlleleCallEvaluator).