change_log.txt

Major changes to ClipKIT are summarized here.

2.2.3
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 through 2.1.0
Introduce and refactor MSA class. Rely on Numpy functionality to accelerate processes.

1.3.0
long description of sequences, rather than identifiers, are kept in the ClipKIT output

1.1.5
carried over code base to biopython, v1.79

1.1.0
smart-gap trimming is introduced and is now the default trimming approach used in ClipKIT.
smart-gap trimming is a dynamic approach to determine the appropriate gaps threshold for an alignment.