Fixed gap character handling. The help message was incongruent with what was happening underneath the hood.
2.2.1
Removed "Processing" block from CLI output. Reordered CLI output to put user arguments first followed by outputs. Added original length of the alignment to output statistics.
2.2.0
Incorporated C3 trimming, which can be evoked using the c3 trimming mode.
2.1.2
Incorporate codon-based trimming. When one position in a codon gets trimmed based on the mode being used, the whole codon will get trimmed from the alignment.
2.0.0
Introduce and refactor MSA class. Rely on Numpy functionality to accelerate processes.